From c17661b22323a66090ea91e04751aa17461b17c5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 11:14:10 +0100 Subject: [PATCH] JAL-1645 reformat help html - 2 spaces indents, no tabs --- help/html/calculations/consensus.html | 70 +- help/html/calculations/conservation.html | 74 +- help/html/calculations/pairwise.html | 40 +- help/html/calculations/pca.html | 202 +-- help/html/calculations/quality.html | 54 +- help/html/calculations/recoverInputdata.html | 20 +- help/html/calculations/redundancy.html | 22 +- help/html/calculations/referenceseq.html | 4 +- help/html/calculations/scorematrices.html | 1633 ++++++++++++++++++++-- help/html/calculations/sorting.html | 116 +- help/html/calculations/structureconsensus.html | 53 +- help/html/calculations/tree.html | 127 +- help/html/calculations/treeviewer.html | 195 +-- help/html/colourSchemes/abovePID.html | 18 +- help/html/colourSchemes/annotationColouring.html | 135 +- help/html/colourSchemes/blosum.html | 15 +- help/html/colourSchemes/buried.html | 82 +- help/html/colourSchemes/clustal.html | 124 +- help/html/colourSchemes/conservation.html | 55 +- help/html/colourSchemes/helix.html | 82 +- help/html/colourSchemes/hydrophobic.html | 89 +- help/html/colourSchemes/index.html | 704 +++++----- help/html/colourSchemes/nucleotide.html | 29 +- help/html/colourSchemes/pid.html | 47 +- help/html/colourSchemes/purinepyrimidine.html | 25 +- help/html/colourSchemes/rnahelicesColouring.html | 65 +- help/html/colourSchemes/strand.html | 82 +- help/html/colourSchemes/taylor.html | 80 +- help/html/colourSchemes/textcolour.html | 32 +- help/html/colourSchemes/turn.html | 82 +- help/html/colourSchemes/user.html | 58 +- help/html/colourSchemes/zappo.html | 75 +- help/html/editing/index.html | 137 +- help/html/features/annotationsFormat.html | 527 ++++--- help/html/features/bioJsonFormat.html | 6 +- help/html/features/chimera.html | 352 +++-- help/html/features/clarguments.html | 404 +++--- help/html/features/codingfeatures.html | 21 +- help/html/features/columnFilterByAnnotation.html | 13 +- help/html/features/commandline.html | 76 +- help/html/features/creatinFeatures.html | 69 +- help/html/features/cursorMode.html | 108 +- help/html/features/dasfeatures.html | 83 +- help/html/features/dassettings.html | 78 +- help/html/features/editingFeatures.html | 50 +- help/html/features/featuresFormat.html | 296 ++-- help/html/features/featureschemes.html | 124 +- help/html/features/featuresettings.html | 176 ++- help/html/features/groovy.html | 129 +- help/html/features/hiddenRegions.html | 161 ++- help/html/features/jalarchive.html | 28 +- help/html/features/jmol.html | 424 +++--- help/html/features/multipleViews.html | 121 +- help/html/features/newkeystrokes.html | 61 +- help/html/features/overview.html | 23 +- help/html/features/pdbsequencefetcher.html | 73 +- help/html/features/pdbviewer.html | 283 ++-- help/html/features/preferences.html | 483 ++++--- help/html/features/search.html | 186 +-- help/html/features/seqfeatures.html | 142 +- help/html/features/seqfetch.html | 83 +- help/html/features/seqmappings.html | 34 +- help/html/features/splitView.html | 118 +- help/html/features/structurechooser.html | 160 ++- help/html/features/varna.html | 114 +- help/html/features/viewingpdbs.html | 189 +-- help/html/features/wrap.html | 622 ++++---- help/html/features/xsspannotation.html | 132 +- help/html/index.html | 131 +- help/html/io/export.html | 61 +- help/html/io/exportseqreport.html | 46 +- help/html/io/fileformats.html | 129 +- help/html/io/index.html | 129 +- help/html/io/modellerpir.html | 61 +- help/html/io/tcoffeescores.html | 26 +- help/html/keys.html | 553 ++++---- help/html/memory.html | 202 +-- help/html/menus/alignmentMenu.html | 1192 ++++++++-------- help/html/menus/alwannotation.html | 114 +- help/html/menus/alwannotationpanel.html | 166 +-- help/html/menus/alwcalculate.html | 131 +- help/html/menus/alwcolour.html | 79 +- help/html/menus/alwedit.html | 165 ++- help/html/menus/alwfile.html | 208 +-- help/html/menus/alwformat.html | 101 +- help/html/menus/alwselect.html | 82 +- help/html/menus/alwview.html | 87 +- help/html/menus/desktopMenu.html | 219 +-- help/html/menus/index.html | 37 +- help/html/menus/popupMenu.html | 318 +++-- help/html/menus/wsmenu.html | 152 +- help/html/misc/aaproperties.html | 37 +- help/html/misc/aminoAcids.html | 514 ++++--- help/html/misc/geneticCode.html | 138 +- help/html/na/index.html | 139 +- help/html/privacy.html | 112 +- help/html/vamsas/index.html | 241 ++-- help/html/webServices/AACon.html | 92 +- help/html/webServices/JABAWS.html | 93 +- help/html/webServices/RNAalifold.html | 117 +- help/html/webServices/dbreffetcher.html | 115 +- help/html/webServices/index.html | 127 +- help/html/webServices/jnet.html | 200 +-- help/html/webServices/msaclient.html | 116 +- help/html/webServices/newsreader.html | 44 +- help/html/webServices/proteinDisorder.html | 438 +++--- help/html/webServices/shmr.html | 88 +- help/html/webServices/urllinks.html | 142 +- help/html/webServices/webServicesParams.html | 134 +- help/html/webServices/webServicesPrefs.html | 137 +- 110 files changed, 10561 insertions(+), 7427 deletions(-) diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index ef3e33a..0a0214e 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -19,34 +19,50 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment Consensus Annotation + +Alignment Consensus Annotation + -

Alignment Consensus Annotation

-

The consensus displayed below the alignment is the percentage of the modal - residue per column. By default this calculation includes gaps in columns. - You can choose to ignore gaps in the calculation by right clicking on the label - "Consensus" to the left of the consensus bar chart. -

If the modal value is shared by more than 1 residue, a "+" symbol - is used in the display for the simple reason that it is not possible to display - multiple characters in a single character space. -

Copying the consensus sequence

-

Select the "Copy Consensus Sequence" entry from -the consensus annotation label to copy the alignment's consensus sequence to the -clipboard. +

+ Alignment Consensus Annotation +

+

The consensus displayed below the alignment is the percentage + of the modal residue per column. By default this calculation + includes gaps in columns. You can choose to ignore gaps in the + calculation by right clicking on the label "Consensus" to + the left of the consensus bar chart. +

If the modal value is shared by more than 1 residue, a + "+" symbol is used in the display for the simple reason + that it is not possible to display multiple characters in a single + character space. +

+ Copying the consensus sequence +

+

+ Select the "Copy Consensus Sequence" + entry from the consensus annotation label to copy the alignment's + consensus sequence to the clipboard. +

+ Sequence logo +

+ By clicking on the label you can also activate the sequence logo. It + indicates the relative amount of residues per column which can be + estimated by its size in the logo. The tooltip of a column gives the + exact numbers for all occurring residues. +
If columns of the alignment are very diverse, then it can + sometimes be difficult to see the sequence logo - in this case, right + click on the annotation row label and select + Normalise Consensus Logo to scale all columns of the + logo to the same height. -

Sequence logo

- By clicking on the label you can also activate the sequence logo. It - indicates the relative amount of residues per column which can be - estimated by its size in the logo. The tooltip of a column gives the - exact numbers for all occurring residues. -
If columns of the alignment are very diverse, then it can - sometimes be difficult to see the sequence logo - in this case, right - click on the annotation row label and select - Normalise Consensus Logo to scale all columns of the - logo to the same height. - -

cDNA Consensus

-A Split Frame View of cDNA and Protein alignments will show the consensus for cDNA below the protein alignment.
-This may provide additional information on mutations in DNA that is not visible in the peptide alignment. +

+ cDNA Consensus +

+ A + Split Frame View of cDNA and + Protein alignments will show the consensus for cDNA below the protein + alignment. +
This may provide additional information on mutations in DNA + that is not visible in the peptide alignment. diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index cb3e785..df8b5ff 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -19,31 +19,43 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment Conservation Annotation -

Alignment Conservation Annotation

-

This is an automatically calculated quantitative alignment -annotation which measures the number of conserved physico-chemical -properties conserved for each column of the alignment. Its calculation -is based on the one used in - the AMAS method of multiple sequence alignment analysis :
-

    Livingstone - C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy - for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 - No. 6 (745-756)). -
-View an HTML version of the paper -

-

Conservation is measured as a numerical index reflecting the conservation of - physico-chemical - properties in the alignment: Identities score highest, and the next most - conserved group contain substitutions to amino acids lying in the same physico-chemical - class.

-

Conservation is visualised on the alignment or a sequence group - as a histogram giving the score for each column. Conserved columns are - indicated by '*' (score of 11 with default amino acid property - grouping), and columns with mutations where all properties are - conserved are marked with a '+' (score of 10, indicating all - properties are conserved).

+ +Alignment Conservation Annotation + + +

+ Alignment Conservation Annotation +

+

+ This is an automatically calculated quantitative alignment + annotation which measures the number of conserved physico-chemical + properties conserved for each column of the alignment. Its + calculation is based on the one used in the AMAS method of multiple + sequence alignment analysis :
+

    + Livingstone C.D. and Barton G.J. (1993), Protein Sequence + Alignments: A Strategy for the Hierarchical Analysis of Residue + Conservation. + CABIOS Vol. + 9 No. 6 (745-756)). +
+ View an HTML version of the paper +

+

+ Conservation is measured as a numerical index reflecting the + conservation of physico-chemical + properties in the alignment: Identities score highest, and the + next most conserved group contain substitutions to amino acids lying + in the same physico-chemical class. +

+

Conservation is visualised on the alignment or a sequence group + as a histogram giving the score for each column. Conserved columns + are indicated by '*' (score of 11 with default amino acid property + grouping), and columns with mutations where all properties are + conserved are marked with a '+' (score of 10, indicating all + properties are conserved).

Mousing over a conservation histogram reveals a tooltip which contains a series of symbols corresponding to the physicochemical @@ -52,10 +64,12 @@ is based on the one used in that the lack of a particular physicochemical property is conserved (e.g. !proline).

-

Colouring an alignment by conservation
-Conservation scores can be used to colour an alignment. This is -explained further in the help page for conservation colouring. -

+

+ Colouring an alignment by conservation
+ Conservation scores can be used to colour an alignment. This is + explained further in the help page for conservation colouring. +

diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 48cebdf..bb80b84 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -19,22 +19,30 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Pairwise Alignment + +Pairwise Alignment + -

Pairwise alignment (Proteins only)

-

This calculation is performed on the selected sequences only. Java is not the - fastest language in the world and aligning more than a handful of sequences - will take a fair amount of time.
- For each pair of sequences the best global alignment is found using BLOSUM62 - as the scoring matrix. The scores reported are the raw scores. The sequences - are aligned using a dynamic programming technique and using the following gap - penalties :

-

Gap open : 12
- Gap extend : 2

-

When you select the pairwise alignment option a new window will come up which - will display the alignments in a text format as they are calculated. Also displayed - is information about the alignment such as alignment score, length and percentage - identity between the sequences.

-

 

+

+ Pairwise alignment (Proteins only) +

+

+ This calculation is performed on the selected sequences only. Java + is not the fastest language in the world and aligning more than a + handful of sequences will take a fair amount of time.
For + each pair of sequences the best global alignment is found using + BLOSUM62 as the scoring matrix. The scores reported are the raw + scores. The sequences are aligned using a dynamic programming + technique and using the following gap penalties : +

+

+ Gap open : 12
Gap extend : 2 +

+

When you select the pairwise alignment option a new window will + come up which will display the alignments in a text format as they + are calculated. Also displayed is information about the alignment + such as alignment score, length and percentage identity between the + sequences.

+

 

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 86097ea..071a2b5 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -23,97 +23,123 @@ Principal Component Analysis -

Principal Component Analysis

-

This calculation creates a spatial representation of the -similarities within a selected group, or all of the sequences in an -alignment. After the calculation finishes, a 3D viewer displays the set -of sequences as points in 'similarity space', and similar sequences tend -to lie near each other in the space.

-

Caveats
The calculation is computationally expensive, and may fail -for very large sets of sequences - usually because the JVM has run out -of memory. A future release of Jalview will be able to avoid this by -executing the calculation via a web service.

+

+ Principal Component Analysis +

+

This calculation creates a spatial representation of the + similarities within a selected group, or all of the sequences in an + alignment. After the calculation finishes, a 3D viewer displays the + set of sequences as points in 'similarity space', and similar + sequences tend to lie near each other in the space.

+

+ Caveats
The calculation is computationally expensive, + and may fail for very large sets of sequences - usually because the + JVM has run out of memory. A future release of Jalview will be able + to avoid this by executing the calculation via a web service. +

-

About PCA

-

Principal components analysis is a technique for examining the -structure of complex data sets. The components are a set of dimensions -formed from the measured values in the data set, and the principal -component is the one with the greatest magnitude, or length. The sets of -measurements that differ the most should lie at either end of this -principal axis, and the other axes correspond to less extreme patterns -of variation in the data set.

+

+ About PCA +

+

Principal components analysis is a technique for examining the + structure of complex data sets. The components are a set of + dimensions formed from the measured values in the data set, and the + principal component is the one with the greatest magnitude, or + length. The sets of measurements that differ the most should lie at + either end of this principal axis, and the other axes correspond to + less extreme patterns of variation in the data set.

-

- Calculating PCAs for aligned sequences
Jalview can - perform PCA analysis on both proteins and nucleotide sequence - alignments. In both cases, components are generated by an eigenvector - decomposition of the matrix formed from the sum of substitution matrix - scores at each aligned position between each pair of sequences - - computed with one of the available score matrices, such as - BLOSUM62, PAM250, or the simple single - nucleotide substitution matrix. The options available for - calculation are given in the - Change Parameters menu.

-

- PCA Calculation modes
- The default Jalview calculation mode - (indicated when Jalview PCA Calculation is - ticked in the Change Parameters menu) is to - perform a PCA on a matrix where elements in the upper diagonal give - the sum of scores for mutating in one direction, and the lower - diagonal is the sum of scores for mutating in the other. For protein - substitution models like BLOSUM62, this gives an asymmetric matrix, - and a different PCA to a matrix produced with the method described in the - paper by G. Casari, C. Sander and A. Valencia. Structural Biology - volume 2, no. 2, February 1995 (pubmed) - and implemented at the SeqSpace server at the EBI. This method - preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the Jalview - PCA Calculation option in the Change - Parameters menu. -

- -

The PCA Viewer

-

This is an interactive display of the sequences positioned within -the similarity space, as points in a rotateable 3D scatterplot. The -colour of each sequence point is the same as the sequence group colours, -white if no colour has been defined for the sequence, and green if the -sequence is part of a the currently selected group.

-

The 3d view can be rotated by dragging the mouse with the left -mouse button pressed. The view can also be zoomed in and out with the up -and down arrow keys (and the roll bar of the mouse if -present). Labels will be shown for each sequence if the entry in the -View menu is checked, and the plot background colour changed from the -View→Background Colour.. dialog box. The File menu allows the view -to be saved (File→Save submenu) as an EPS or PNG -image or printed, and the original alignment data and matrix resulting -from its PCA analysis to be retrieved. The coordinates for the whole PCA -space, or just the current view may also be exported as CSV files for -visualization in another program or further analysis.

-

Options for coordinates export are:

-
    -
  • Output Values - complete dump of analysis (TxT* matrix computed from sum of scores for all pairs of aligned residues from from i->j and j->i, conditioned matrix to be diagonalised, tridiagonal form, major eigenvalues found)
    • -
  • Output Points - The eigenvector matrix - rows correspond to sequences, columns correspond to each dimension in the PCA
    • -
  • Transformed Points - The 3D coordinates for each sequence as shown in the PCA plot
+

+ Calculating PCAs for aligned sequences
Jalview can + perform PCA analysis on both proteins and nucleotide sequence + alignments. In both cases, components are generated by an + eigenvector decomposition of the matrix formed from the sum of + substitution matrix scores at each aligned position between each + pair of sequences - computed with one of the available score + matrices, such as BLOSUM62, + PAM250, or the simple single nucleotide substitution matrix. The options + available for calculation are given in the Change + Parameters menu. +

+

+ PCA Calculation modes
The default Jalview calculation + mode (indicated when Jalview PCA + Calculation is ticked in the Change + Parameters menu) is to perform a PCA on a matrix where elements + in the upper diagonal give the sum of scores for mutating in one + direction, and the lower diagonal is the sum of scores for mutating + in the other. For protein substitution models like BLOSUM62, this + gives an asymmetric matrix, and a different PCA to a matrix produced + with the method described in the paper by G. Casari, C. Sander and + A. Valencia. Structural Biology volume 2, no. 2, February 1995 (pubmed) and implemented at the SeqSpace server at the EBI. This + method preconditions the matrix by multiplying it with its + transpose, and can be employed in the PCA viewer by unchecking the Jalview + PCA Calculation option in the Change + Parameters menu. +

+ +

+ The PCA Viewer +

+

This is an interactive display of the sequences positioned + within the similarity space, as points in a rotateable 3D + scatterplot. The colour of each sequence point is the same as the + sequence group colours, white if no colour has been defined for the + sequence, and green if the sequence is part of a the currently + selected group.

+

+ The 3d view can be rotated by dragging the mouse with the left + mouse button pressed. The view can also be zoomed in and out with + the up and down arrow keys (and the roll bar of the + mouse if present). Labels will be shown for each sequence if the + entry in the View menu is checked, and the plot background colour + changed from the View→Background Colour.. dialog box. The File + menu allows the view to be saved (File→Save + submenu) as an EPS or PNG image or printed, and the original + alignment data and matrix resulting from its PCA analysis to be + retrieved. The coordinates for the whole PCA space, or just the + current view may also be exported as CSV files for visualization in + another program or further analysis. +

+

Options for coordinates export are:

+
    +
  • Output Values - complete dump of analysis (TxT* matrix + computed from sum of scores for all pairs of aligned residues from + from i->j and j->i, conditioned matrix to be diagonalised, + tridiagonal form, major eigenvalues found)
    • +
  • Output Points - The eigenvector matrix - rows correspond to + sequences, columns correspond to each dimension in the PCA
    • +
  • Transformed Points - The 3D coordinates for each sequence + as shown in the PCA plot
    • +
-

A tool tip gives the sequence ID corresponding to a point in the -space, and clicking a point toggles the selection of the corresponding -sequence in the associated alignment window views. By default, -points are only associated with the alignment view from which the PCA -was calculated, but this may be changed via the View→Associate -Nodes sub-menu.

-

Initially, the display shows the first three components of the -similarity space, but any eigenvector can be used by changing the -selected dimension for the x, y, or z axis through each ones menu -located below the 3d display. The Reset button will reset axis and rotation settings to their defaults.

-

-

-The output of points and transformed point coordinates was added to the Jalview desktop in v2.7. -The Reset button and Change Parameters menu were added in Jalview 2.8. -Support for PAM250 based PCA was added in Jalview 2.8.1. +left-clicking and dragging the mouse over the display. --> + By default, points are only associated with the alignment view from + which the PCA was calculated, but this may be changed via the View→Associate + Nodes sub-menu. +

+

+ Initially, the display shows the first three components of the + similarity space, but any eigenvector can be used by changing the + selected dimension for the x, y, or z axis through each ones menu + located below the 3d display. The Reset + button will reset axis and rotation settings to their defaults. +

+

+

+ The output of points and transformed point coordinates was + added to the Jalview desktop in v2.7. The Reset button + and Change Parameters menu were added in Jalview 2.8. Support + for PAM250 based PCA was added in Jalview 2.8.1. diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 7bc4d75..4f05b06 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -19,34 +19,34 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment Quality Annotation + +Alignment Quality Annotation + -

Alignment Quality Annotation

-

Alignment Quality is one of the automatically calculated -quantitative alignment -annotations displayed below the columns of a multiple sequence -alignment (and can be used to shade the alignment). It is an ad-hoc -measure of the likelihood of observing the mutations (if any) in a -particular column of the alignment.

-

-More precisely, the quality score is inversely proportional to the -average cost of all pairs of mutations observed in a particular column -of the alignment - a high alignment quality score for a column would -suggest that there are no mutations, or most mutations observed are -favourable. -

+

+ Alignment Quality Annotation +

+

Alignment Quality is one of the automatically calculated + quantitative alignment annotations displayed below the columns of a + multiple sequence alignment (and can be used to shade the + alignment). It is an ad-hoc measure of the likelihood of observing + the mutations (if any) in a particular column of the alignment.

+

More precisely, the quality score is inversely proportional to + the average cost of all pairs of mutations observed in a particular + column of the alignment - a high alignment quality score for a + column would suggest that there are no mutations, or most mutations + observed are favourable.

-

The Algorithm
-The quality score is calculated for each column in an alignment by -summing, for all mutations, the ratio of the two BLOSUM 62 scores for -a mutation pair and each residue's conserved BLOSUM62 score (which -is higher). This value is normalised for each column, and then plotted -on a scale from 0 to 1. -

-

-Multiple alignment algorithms using the BLOSUM 62 substition matrices -should, in theory, maximise alignment quality for an un-gapped -alignment, and locally maximise quality for gapped alignments. -

+

+ The Algorithm
The quality score is calculated for + each column in an alignment by summing, for all mutations, the ratio + of the two BLOSUM 62 scores for a mutation pair and each residue's + conserved BLOSUM62 score (which is higher). This value is normalised + for each column, and then plotted on a scale from 0 to 1. +

+

Multiple alignment algorithms using the BLOSUM 62 substition + matrices should, in theory, maximise alignment quality for an + un-gapped alignment, and locally maximise quality for gapped + alignments.

diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html index ec831c9..5d17cc3 100644 --- a/help/html/calculations/recoverInputdata.html +++ b/help/html/calculations/recoverInputdata.html @@ -19,15 +19,19 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Viewing Input Data to PCA and Tree calculations + +Viewing Input Data to PCA and Tree calculations + -

Viewing Input Data to PCA and Tree calculations

-

It is always possible to retrieve the input data used to calculate - a tree or PCA plot by using the analysis window's - "File - -> Input Data..." menu item. The Input Data will be - shown in a new alignment window, with any hidden columns - preserved.

+

+ Viewing Input Data to PCA and Tree calculations +

+

+ It is always possible to retrieve the input data used to calculate a + tree or PCA plot by using the analysis window's "File + -> Input Data..." menu item. The Input Data will be shown + in a new alignment window, with any hidden columns preserved. +

diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index 254ae53..94cbc65 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -23,14 +23,18 @@ Removing Redundancy -

Removing redundancy

-

Selecting the option in the Alignment window's Edit -menu or pressing 'CONTROL+D' brings up a dialog box -asking you to select a threshold. If the percentage identity between the -aligned positions of any two sequences in the visible alignment exceeds -this value, the shorter sequence is discarded.
Note: The redundancy -calculation is done when the dialog box is opened. For large numbers -of sequences this can take a long time as all pairs have to be compared. -

+

+ Removing redundancy +

+

+ Selecting the option in the Alignment window's Edit + menu or pressing 'CONTROL+D' brings up a dialog box + asking you to select a threshold. If the percentage identity between + the aligned positions of any two sequences in the visible alignment + exceeds this value, the shorter sequence is discarded.
+ Note: The redundancy calculation is done when the dialog + box is opened. For large numbers of sequences this can take a long + time as all pairs have to be compared. +

diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html index 27d2cd2..03d24a5 100644 --- a/help/html/calculations/referenceseq.html +++ b/help/html/calculations/referenceseq.html @@ -35,8 +35,8 @@

  • Jalview automatically assigns a reference sequence when JPred4 predictions are - imported. + href="../webServices/jnet.html" + >JPred4 predictions are imported.
  • Assigning a reference sequence
    A sequence can be marked as the reference sequence by right-clicking diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index 2857723..5fb900f 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -23,99 +23,1548 @@ Substitution matrices in Jalview -Substitution Matrices available in Jalview -

    Jalview includes a small number of built in substitution matrices, used for different types of analysis.

    -
      -
    • BLOSUM62 is the standard protein sequence alignment and analysis matrix.
      • -
    • PAM250 is another standard protein matrix, and (since 2.8.1) is available for Tree and PCA calculations.
      • -
    • Simple Nucleotide Substition is a (fairly) arbitrary DNA/RNA substitution matrix.
      • - -
    +
-

BLOSUM62
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A4-20-2-1-20-2-1-1-1-1-2-1-1-11000-30-2-1
B-24-341-3-10-30-4-33-20-10-1-1-3-4-1-31
C0-39-3-4-2-3-3-1-3-1-1-3-3-33-1-1-2-1-2-2-2-3
D-24-362-3-1-1-3-1-4-31-10-20-1-1-3-4-1-31
E-11-425-3-20-31-3-20-1200-1-1-2-3-1-24
F-2-3-2-3-36-3-10-300-3-4-3-3-2-2-1-11-13-3
G0-1-3-1-2-36-2-4-2-4-30-2-2-20-2-1-3-2-1-3-2
H-20-3-10-1-28-3-1-3-21-200-1-2-1-3-2-120
I-1-3-1-3-30-4-34-321-3-3-3-3-2-1-13-3-1-1-3
K-10-3-11-3-2-1-35-2-10-1120-1-1-2-3-1-21
L-1-4-1-4-30-4-32-242-3-3-2-2-2-1-11-2-1-1-3
M-1-3-1-3-20-3-21-125-2-20-1-1-1-11-1-1-1-1
N-23-310-301-30-3-26-20010-1-3-4-1-20
P-1-2-3-1-1-4-2-2-3-1-3-2-27-1-2-1-1-2-2-4-2-3-1
Q-10-302-3-20-31-200-1510-1-1-2-2-1-13
R-1-1-3-20-3-20-32-2-10-215-1-1-1-3-3-1-20
S10-100-20-1-20-2-11-10-1410-2-30-20
T0-1-1-1-1-2-2-2-1-1-1-10-1-1-11500-20-2-1
U0-1-2-1-1-1-1-1-1-1-1-1-1-2-1-100-1-1-2-1-1-1
V0-3-1-3-2-1-3-33-211-3-2-2-3-20-14-3-1-1-2
W-3-4-2-4-31-2-2-3-3-2-1-4-4-2-3-3-2-2-311-22-3
X0-1-2-1-1-1-1-1-1-1-1-1-1-2-1-100-1-1-2-1-1-1
Y-2-3-2-3-23-32-1-2-1-1-2-3-1-2-2-2-1-12-17-2
Z-11-314-3-20-31-3-10-1300-1-1-2-3-1-24
-

PAM250
-Percentage Accepted Mutation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).
-Jalview 2.8.1 introduced support for PAM250 based PCA and tree calculations. - - - - - - - - - - - - - - - - - - - - - - - - - - -
 A  B  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  U  V  W  X  Y  Z 
A20-200-31-1-1-1-2-1010-21100-60-30
B03-433-401-21-3-22-11-100-1-2-5-1-32
C-2-412-5-5-4-3-3-2-5-6-5-4-3-5-40-2-3-2-8-30-5
D03-543-611-20-4-32-12-100-1-2-7-1-43
E03-534-501-20-3-21-12-100-1-2-7-1-43
F-3-4-4-6-59-5-21-520-3-5-5-4-3-3-2-10-27-5
G10-310-55-2-3-2-4-300-1-310-1-1-7-1-50
H-11-311-2-26-20-2-22032-1-1-1-2-3-102
I-1-2-2-2-21-3-25-222-2-2-2-2-10-14-5-1-1-2
K-11-500-5-20-25-301-11300-1-2-3-1-40
L-2-3-6-4-32-4-22-364-3-3-2-3-3-2-12-2-1-1-3
M-1-2-5-3-20-3-22046-2-2-10-2-1-12-4-1-2-2
N02-421-302-21-3-22010100-2-40-21
P1-1-3-1-1-500-2-1-3-2060010-1-1-6-1-50
Q01-522-5-13-21-2-11041-1-1-1-2-5-1-43
R-2-1-4-1-1-4-32-23-3000160-1-1-22-1-40
S10000-31-1-10-3-211-10210-1-20-30
T10-200-30-100-2-100-1-11300-50-3-1
U0-1-3-1-1-2-1-1-1-1-1-10-1-1-100-1-1-4-1-2-1
V0-2-2-2-2-1-1-24-222-2-1-2-2-10-14-6-1-2-2
W-6-5-8-7-70-7-3-5-3-2-4-4-6-52-2-5-4-617-40-6
X0-1-3-1-1-2-1-1-1-1-1-10-1-1-100-1-1-4-1-2-1
Y-3-30-4-47-50-1-4-1-2-2-5-4-4-3-3-2-20-210-4
Z02-533-502-20-3-210300-1-1-2-6-1-43
+

+ BLOSUM62
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 A  B  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  U  V  W  X  Y  Z 
A4-20-2-1-20-2-1-1-1-1-2-1-1-11000-30-2-1
B-24-341-3-10-30-4-33-20-10-1-1-3-4-1-31
C0-39-3-4-2-3-3-1-3-1-1-3-3-33-1-1-2-1-2-2-2-3
D-24-362-3-1-1-3-1-4-31-10-20-1-1-3-4-1-31
E-11-425-3-20-31-3-20-1200-1-1-2-3-1-24
F-2-3-2-3-36-3-10-300-3-4-3-3-2-2-1-11-13-3
G0-1-3-1-2-36-2-4-2-4-30-2-2-20-2-1-3-2-1-3-2
H-20-3-10-1-28-3-1-3-21-200-1-2-1-3-2-120
I-1-3-1-3-30-4-34-321-3-3-3-3-2-1-13-3-1-1-3
K-10-3-11-3-2-1-35-2-10-1120-1-1-2-3-1-21
L-1-4-1-4-30-4-32-242-3-3-2-2-2-1-11-2-1-1-3
M-1-3-1-3-20-3-21-125-2-20-1-1-1-11-1-1-1-1
N-23-310-301-30-3-26-20010-1-3-4-1-20
P-1-2-3-1-1-4-2-2-3-1-3-2-27-1-2-1-1-2-2-4-2-3-1
Q-10-302-3-20-31-200-1510-1-1-2-2-1-13
R-1-1-3-20-3-20-32-2-10-215-1-1-1-3-3-1-20
S10-100-20-1-20-2-11-10-1410-2-30-20
T0-1-1-1-1-2-2-2-1-1-1-10-1-1-11500-20-2-1
U0-1-2-1-1-1-1-1-1-1-1-1-1-2-1-100-1-1-2-1-1-1
V0-3-1-3-2-1-3-33-211-3-2-2-3-20-14-3-1-1-2
W-3-4-2-4-31-2-2-3-3-2-1-4-4-2-3-3-2-2-311-22-3
X0-1-2-1-1-1-1-1-1-1-1-1-1-2-1-100-1-1-2-1-1-1
Y-2-3-2-3-23-32-1-2-1-1-2-3-1-2-2-2-1-12-17-2
Z-11-314-3-20-31-3-10-1300-1-1-2-3-1-24
+

+ PAM250
Percentage + Accepted Mutation matrix. PAM250 + estimates substitutions after 250% of sites have changed (each + site can be mutated multple times).
Jalview 2.8.1 introduced + support for PAM250 based PCA + and tree calculations. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 A  B  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  U  V  W  X  Y  Z 
A20-200-31-1-1-1-2-1010-21100-60-30
B03-433-401-21-3-22-11-100-1-2-5-1-32
C-2-412-5-5-4-3-3-2-5-6-5-4-3-5-40-2-3-2-8-30-5
D03-543-611-20-4-32-12-100-1-2-7-1-43
E03-534-501-20-3-21-12-100-1-2-7-1-43
F-3-4-4-6-59-5-21-520-3-5-5-4-3-3-2-10-27-5
G10-310-55-2-3-2-4-300-1-310-1-1-7-1-50
H-11-311-2-26-20-2-22032-1-1-1-2-3-102
I-1-2-2-2-21-3-25-222-2-2-2-2-10-14-5-1-1-2
K-11-500-5-20-25-301-11300-1-2-3-1-40
L-2-3-6-4-32-4-22-364-3-3-2-3-3-2-12-2-1-1-3
M-1-2-5-3-20-3-22046-2-2-10-2-1-12-4-1-2-2
N02-421-302-21-3-22010100-2-40-21
P1-1-3-1-1-500-2-1-3-2060010-1-1-6-1-50
Q01-522-5-13-21-2-11041-1-1-1-2-5-1-43
R-2-1-4-1-1-4-32-23-3000160-1-1-22-1-40
S10000-31-1-10-3-211-10210-1-20-30
T10-200-30-100-2-100-1-11300-50-3-1
U0-1-3-1-1-2-1-1-1-1-1-10-1-1-100-1-1-4-1-2-1
V0-2-2-2-2-1-1-24-222-2-1-2-2-10-14-6-1-2-2
W-6-5-8-7-70-7-3-5-3-2-4-4-6-52-2-5-4-617-40-6
X0-1-3-1-1-2-1-1-1-1-1-10-1-1-100-1-1-4-1-2-1
Y-3-30-4-47-50-1-4-1-2-2-5-4-4-3-3-2-20-210-4
Z02-533-502-20-3-210300-1-1-2-6-1-43
-

Simple Nucleotide Substitution
-This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA. -In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other. - - - - - - - - - - - - -
 A  C  G  I  N  R  T  U  X  Y 
A10-8-8111-8-81-8
C-810-811-8-8-811
G-8-810111-8-81-8
I11110101100
N11111011111
R1-810110-8-80-8
T-8-8-811-8101011
U-8-8-811-8101011
X11101011100
Y-81-801-811010
-This nucleotide matrix was introduced in - Jalview 2.8. If you'd like to improve it - please take a look at Issue JAL-1027 - - introduce a nucleotide substitution matrix that supports RNA/DNA - and ambiguity codes - -

- - - + + diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index 51e9fa3..8c017a9 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -23,53 +23,75 @@ Sorting Sequences -

Sorting Sequences

-

Any group of selected sequences may be reordered by pressing the -up or down arrow keys. The whole alignment may also be reordered by -the use of the functions in the Sort menu (Calculate→Sort): -

-
    -

  • Sort by ID

    -

    Orders the sequences by the alphanumeric (0-9A-Za-z) -precedence of their names.

    -

    • -

  • Sort by Group

    -

    Places sequences in the same group adjacent to each other.

    -

    • -

  • Sort by Pairwise Identity

    -

    Places pairs of sequences together that align with the greatest -fraction of conserved residues. -

    -

    • -

  • Sort by Tree Order

    -

    The leaf ordering of a particular phylogenetic tree is used to -order the sequences corresponding to those leaves in the -alignment.
    -If a tree has been calculated from or associated with the current -alignment, its name will appear in the submenu Sort→By Tree Order.

    -

    • -

  • Sort by alignment ordering

    -

    Multiple alignment methods often order the sequences in their -alignments by some measure of sequence identity.
    -If the current alignment has been generated by one of Jalview's -alignment web services, the alignment ordering can be recovered by -its corresponding entry in the Sort menu. -

    -
    • -

  • Sort by Score

    -

    This menu appears if the alignment contains any sequence associated -alignment annotation with associated score values. Each entry is the -label for a distinct group of sequence associated annotation -scores which can be used for sorting.

    -
-

Reversing the Order

-

Selecting any item from the Sort menu will sort sequences in an -ascending order according to the property defining the sort. If the -same sort is re-applied, the sequences will be sorted in the inverse -order. In the case of trees and alignment orderings, Jalview will -remember your last choice for sorting the alignment and only apply the -inverse ordering if you select the same tree or alignment ordering -item again.

+

+ Sorting Sequences +

+

+ Any group of selected sequences may be reordered by pressing the up + or down arrow keys. The whole alignment may also be reordered by the + use of the functions in the Sort menu (Calculate→Sort): +

+
    +

  • + Sort by ID +

    +

    Orders the sequences by the alphanumeric (0-9A-Za-z) + precedence of their names.

    +

    • +

  • + Sort by Group +

    +

    Places sequences in the same group adjacent to each other.

    +

    • +

  • + Sort by Pairwise Identity +

    +

    Places pairs of sequences together that align with the + greatest fraction of conserved residues.

    +

    • +

  • + Sort by Tree Order +

    +

    + The leaf ordering of a particular phylogenetic tree is used to + order the sequences corresponding to those leaves in the + alignment.
    If a tree has been calculated from or + associated with the current alignment, its name will appear in + the submenu Sort→By Tree Order. +

    +

    • +

  • + Sort by alignment ordering +

    +

    + Multiple alignment methods often order the sequences in their + alignments by some measure of sequence identity.
    If the + current alignment has been generated by one of Jalview's + alignment web services, the alignment ordering can be recovered + by its corresponding entry in the Sort menu. +

    • +

  • + Sort by Score +

    +

    + This menu appears if the alignment contains any sequence associated alignment annotation with associated + score values. Each entry is the label for a distinct group of + sequence associated annotation scores which can be used for + sorting. +

    +
+

+ Reversing the Order +

+

Selecting any item from the Sort menu will sort sequences in an + ascending order according to the property defining the sort. If the + same sort is re-applied, the sequences will be sorted in the inverse + order. In the case of trees and alignment orderings, Jalview will + remember your last choice for sorting the alignment and only apply + the inverse ordering if you select the same tree or alignment + ordering item again.

diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 033f0c0..7325439 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -19,29 +19,36 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment RNA Structure Consensus Annotation -

Alignment RNA Structure Consensus Annotation

+ +Alignment RNA Structure Consensus Annotation + + +

+ Alignment RNA Structure Consensus Annotation +

-

The RNA structure consensus displayed below the alignment is the -percentage of valid base pairs per column. It is calculated in -relation to a secondary structure and just paired columns are -calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and -the wobble base pair (G-T/U) are regarded as valid pairings.
-The amount of valid base pairs is indicated by the profile in the -Alignment Annotation row.
-By default this calculation includes gaps in columns. You can choose -to ignore gaps in the calculation by right clicking on the label -"StrConsensus" to the left of the structure consensus bar -chart.
- -

Structure logo

-By clicking on the label you can also activate the structure logo. It is very -similar to a sequence logo but counts the numbers of base pairs. There -are two residues per column, the actual column and the interacting -base. The opening bracket is always the one on the left side.
-Like sequence logos the relative amount of a specific base pair can be -estimated by its size in the logo. The tool tip of a column gives the -exact numbers for all occurring valid base pairs. -

+

+ The RNA structure consensus displayed below the alignment is the + percentage of valid base pairs per column. It is calculated in + relation to a secondary structure and just paired columns are + calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) + and the wobble base pair (G-T/U) are regarded as valid pairings.
+ The amount of valid base pairs is indicated by the profile in the + Alignment Annotation row.
By default this calculation + includes gaps in columns. You can choose to ignore gaps in the + calculation by right clicking on the label "StrConsensus" + to the left of the structure consensus bar chart.
+

+ Structure logo +

+ By clicking on the label you can also activate the structure logo. It + is very similar to a sequence logo but counts the numbers of base + pairs. There are two residues per column, the actual column and the + interacting base. The opening bracket is always the one on the left + side. +
Like sequence logos the relative amount of a specific base + pair can be estimated by its size in the logo. The tool tip of a + column gives the exact numbers for all occurring valid base pairs. +

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 6a31403..7a8271e 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -19,22 +19,27 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Tree Calculation + +Tree Calculation + -

Calculation of trees from alignments

-

Trees are calculated on either the complete alignment, or just the -currently selected group of sequences, using the functions in the -Calculate→Calculate tree submenu. -Once calculated, trees are displayed in a new tree viewing window. There are -four different calculations, using one of two distance measures and -constructing the tree from one of two algorithms : -

-

Distance Measures

-

Trees are calculated on the basis of a measure of similarity -between each pair of sequences in the alignment : - - +

+ Calculation of trees from alignments +

+

+ Trees are calculated on either the complete alignment, or just the + currently selected group of sequences, using the functions in the Calculate→Calculate + tree submenu. Once calculated, trees are displayed in a new tree viewing window. There are four different calculations, using + one of two distance measures and constructing the tree from one of + two algorithms : +

+

+ Distance Measures +

+

Trees are calculated on the basis of a measure of similarity + between each pair of sequences in the alignment :

  • PID
    The percentage identity between the two sequences at each aligned position. @@ -46,13 +51,15 @@ between each pair of sequences in the alignment : residues)'.
-
  • BLOSUM62, PAM250, DNA
    These - options use one of the available substitution matrices to compute - a sum of scores for the residue pairs at each aligned position. -
    • For details about each model, see the - list of built-in score matrices. +
    • BLOSUM62, PAM250, DNA
      These options + use one of the available substitution matrices to compute a sum of + scores for the residue pairs at each aligned position. +
      • +
  • Sequence Feature Similarity
    Trees are constructed from a distance matrix formed from Jaccard distances between sequence features observed at each column of the @@ -73,43 +80,49 @@ between each pair of sequences in the alignment : same type will be grouped together in trees computed with this metric. This measure was introduced in Jalview 2.9
    • -

    Tree Construction Methods

    -

    Jalview currently supports two kinds of agglomerative clustering -methods. These are not intended to substitute for rigorous -phylogenetic tree construction, and may fail on very large alignments. -

      -
    • UPGMA tree
      - UPGMA stands for Unweighted Pair-Group Method using Arithmetic - averages. Clusters are iteratively formed and extended by finding a - non-member sequence with the lowest average dissimilarity over the - cluster members. -

      -
      • -
    • Neighbour Joining tree
      - First described in 1987 by Saitou and Nei, this method applies a - greedy algorithm to find the tree with the shortest branch - lengths.
      - This method, as implemented in Jalview, is considerably more - expensive than UPGMA. -
      • -
    -

    A newly calculated tree will be displayed in a new tree viewing window. In -addition, a new entry with the same tree viewer window name will be added in the Sort -menu so that the alignment can be reordered to reflect the ordering of -the leafs of the tree. If the tree was calculated on a selected region -of the alignment, then the title of the tree view will reflect this.

    +

    + Tree Construction Methods +

    +

    Jalview currently supports two kinds of agglomerative + clustering methods. These are not intended to substitute for + rigorous phylogenetic tree construction, and may fail on very large + alignments. +

      +
    • UPGMA tree
      UPGMA stands for + Unweighted Pair-Group Method using Arithmetic averages. Clusters + are iteratively formed and extended by finding a non-member + sequence with the lowest average dissimilarity over the cluster + members. +

      • +
    • Neighbour Joining tree
      First + described in 1987 by Saitou and Nei, this method applies a greedy + algorithm to find the tree with the shortest branch lengths.
      + This method, as implemented in Jalview, is considerably more + expensive than UPGMA.
      • +
    +

    + A newly calculated tree will be displayed in a new tree viewing window. In addition, a new entry with the same tree + viewer window name will be added in the Sort menu so that the + alignment can be reordered to reflect the ordering of the leafs of + the tree. If the tree was calculated on a selected region of the + alignment, then the title of the tree view will reflect this. +

    -

    External Sources for Phylogenetic Trees

    -

    A number of programs exist for the reliable construction of - phylogenetic trees, which can cope with large numbers of sequences, - use better distance methods and can perform bootstrapping. Jalview - can read Newick - format tree files using the 'Load Associated Tree' entry of the - alignment's File menu. Sequences in the alignment will be - automatically associated to nodes in the tree, by matching Sequence - IDs to the tree's leaf names. +

    + External Sources for Phylogenetic Trees +

    +

    + A number of programs exist for the reliable construction of + phylogenetic trees, which can cope with large numbers of sequences, + use better distance methods and can perform bootstrapping. Jalview + can read Newick format tree files using the 'Load Associated Tree' entry + of the alignment's File menu. Sequences in the alignment will be + automatically associated to nodes in the tree, by matching Sequence + IDs to the tree's leaf names.

    diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index 7ad4f1d..b45f8fe 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -23,98 +23,109 @@ The Tree Viewing Window -

    The Tree Viewing Window

    -

    - The tree viewing window is opened when a tree has been calculated - from an alignment, or imported via a file or web service. It includes menus for - controlling layout and file and figure creation, and enables - various selection and colouring operations on the - associated sequences in the alignment.

    -

    -Selecting Sequence Leaf Nodes
    - Selecting sequence ids at the leaves of the tree selects the - corresponding sequences in the original alignment. These selections - are also reflected in any other analysis windows associated with the - alignment, such as another tree viewer.

    -

    Grouping sequences by partitioning the tree at a particular distanec
    - Clicking anywhere along the extent of the tree (but not on a leaf or - internal node) defines a tree 'partition', by cutting every branch - of the tree spanning the depth where the mouse-click occurred. Groups - are created containing sequences at the leaves of each connected - sub tree. These groups are each given a different colour, which are - reflected in other windows in the same way as if the sequence ids - were selected, and can be edited in the same way as user defined - sequence groups. -

    -

    Tree partitions are useful for comparing clusters produced by -different methods and measures. They are also an effective way of -identifying specific patterns of conservation and mutation -corresponding to the overall phylogenetic structure, when combined -with the conservation -based colour scheme.

    -

    -Selecting Subtrees and changing the branch order and subtree group colour
    -Moving the mouse over an internal node of the tree will highlight - it. You can then :

      -
    • Click the highlighted node to select all the sequences in that branch. -
    • Double-click the highlighted node to rearrange the tree - diagram by inverting the branch ordering at that - node. -
    • Right-click to open the 'Select Sub-Tree Colour' dialog box, to - pick a new colour for the sub-tree and associated sequences. +

      + The Tree Viewing Window +

      +

      + The tree viewing window is opened when a tree has been calculated from an alignment, or imported via a file or web + service. It includes menus for controlling + layout and file and figure creation, and enables various selection + and colouring operations on the associated sequences in the + alignment. +

      +

      + Selecting Sequence Leaf Nodes
      + Selecting sequence ids at the leaves of the tree selects the + corresponding sequences in the original alignment. These selections + are also reflected in any other analysis windows associated with the + alignment, such as another tree viewer. +

      +

      + Grouping sequences by partitioning the + tree at a particular distanec
      Clicking anywhere along + the extent of the tree (but not on a leaf or internal node) defines + a tree 'partition', by cutting every branch of the tree spanning the + depth where the mouse-click occurred. Groups are created containing + sequences at the leaves of each connected sub tree. These groups are + each given a different colour, which are reflected in other windows + in the same way as if the sequence ids were selected, and can be + edited in the same way as user defined sequence groups. +

      +

      + Tree partitions are useful for comparing clusters produced by + different methods and measures. They are also an effective way of + identifying specific patterns of conservation and mutation + corresponding to the overall phylogenetic structure, when combined + with the conservation + based colour scheme. +

      +

      + Selecting Subtrees and changing the branch + order and subtree group colour
      Moving the mouse over an + internal node of the tree will highlight it. You can then : +

        +
      • Click the highlighted node to select all the sequences in + that branch. +
      • Double-click the highlighted node to rearrange the tree + diagram by inverting the branch ordering at that node. +
      • Right-click to open the 'Select Sub-Tree Colour' dialog + box, to pick a new colour for the sub-tree and associated + sequences.
      -

      -

      -File Menu

      -

      This menu allows the displayed tree to be saved as a Newick tree -file (Save→Newick File), printed or exported as an image (PNG) or -Postscript file. Finally, data used to calculate the tree can be -retrieved with the 'Input Data...' entry. -

      -

      View Menu

      -

      When the tree viewer is opened, it displays all the annotation -associated with a tree. Trees calculated by Jalview have branch -lengths, which correspond to the distance measure used to construct -the tree. Tree imported from outside may also contain bootstrap information, -and additional leaves from sequences not present in the associated -alignment. -

      -

      The view menu mostly contains options controlling the way a tree is -rendered and labeled: -

        -
      • Fit to Window

        -The tree layout will be scaled to fit in the display -window. You may need to reduce the font size to minimise the leaf -label overlap when this option is selected. -

        • -
      • Font Size ...n

        -Brings up a dialog box to set the font size for the leaf -names. n is the current font size. -

        • -
      • Show Distances

        -Labels each branch or leaf with its associated branch -length.

        • -
      • Show Bootstrap values

        -Labels each branch or leaf with its associated bootstrap value. -

        • -
      • Mark unlinked leaves

        -Toggles the display of a '*' at the beginning of a leaf label to -indicate that there is no sequence corresponding to that leaf in the -associated alignment. -

        • -
      • Sort Alignment By Tree -

        - Sorts any associated alignment views using the current tree. (Only - available in the Jalview Desktop) -

        -
        • -
      • Associate Leaves with ... -

        - Only visible when there are multiple - views of the same alignment to show and edit which alignment views - are associated with the leaves of the displayed tree. -

        -
      -

      +

      +

      + File Menu +

      +

      This menu allows the displayed tree to be saved as a Newick + tree file (Save→Newick File), printed or exported as an image + (PNG) or Postscript file. Finally, data used to calculate the tree + can be retrieved with the 'Input Data...' entry.

      +

      + View Menu +

      +

      When the tree viewer is opened, it displays all the annotation + associated with a tree. Trees calculated by Jalview have branch + lengths, which correspond to the distance measure used to construct + the tree. Tree imported from outside may also contain bootstrap + information, and additional leaves from sequences not present in the + associated alignment.

      +

      The view menu mostly contains options controlling the way a + tree is rendered and labeled: +

        +
      • Fit to Window +

        The tree layout will be scaled to fit in the display window. + You may need to reduce the font size to minimise the leaf label + overlap when this option is selected.

        • +
      • Font Size ...n +

        + Brings up a dialog box to set the font size for the leaf names. + n is the current font size. +

        • +
      • Show Distances +

        Labels each branch or leaf with its associated branch length.

        • +
      • Show Bootstrap values +

        Labels each branch or leaf with its associated bootstrap + value.

        • +
      • Mark unlinked leaves +

        Toggles the display of a '*' at the beginning of a leaf label + to indicate that there is no sequence corresponding to that leaf + in the associated alignment.

        • +
      • Sort Alignment By Tree +

        + Sorts any associated alignment views using the current tree. (Only + available in the Jalview Desktop) +

        • +
      • Associate Leaves with ... +

        + Only visible when there are multiple views of the same alignment to show and edit which + alignment views are associated with the leaves of the displayed + tree. +

        +
      +

      diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 0ec4c95..614764b 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -19,7 +19,8 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Above PID Colours + +Above PID Colours -

      Colour schemes

      -

      Jalview allows the user to set a background colour for the whole -alignment view or for each group defined on regions within it.

      -

      To change the background colour, simply select the colour from -the "Colour" menu.

      -

      To change the colour of a group, right click on any residue -within a group and use the popup menu to define the group colour.

      -

      At the top of the "Colour" menu the tick box -"Apply Background Colour to all groups". This is ticked by -default so that a chosen colour scheme will be applied to all existing -groups. If you wish to maintain the colour scheme for defined groups, -make sure you deselect this option before changing the background -colour.

      -

      The "Colour→Colour Text..." entry -opens a dialog box to set a different text colour for light and dark -background, and the intensity threshold for transition between them.

      -

      The default colour schemes are summarised in the table below: -

      -

       

      -

      Protein Colour Schemes

      - - - - -
      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      ARNDCQEGHILKMFPSTWYVBXZ
      Clustal
      Zappo
      Taylor
      Hydrophobicity
      Helix Propensity
      Strand Propensity
      Turn Propensity
      Buried Index
      -
      -

       

      -

      Nucleotide Colour Schemes

      - - - - -
      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      A C G T U I X R Y N W S M K B H D V
      Nucleotide
      Purine/Pyrimidine
      -
      +

      + Colour schemes +

      +

      Jalview allows the user to set a background colour for the + whole alignment view or for each group defined on regions within it.

      +

      To change the background colour, simply select the colour from + the "Colour" menu.

      +

      To change the colour of a group, right click on any residue + within a group and use the popup menu to define the group colour.

      +

      At the top of the "Colour" menu the tick box + "Apply Background Colour to all groups". This is ticked by + default so that a chosen colour scheme will be applied to all + existing groups. If you wish to maintain the colour scheme for + defined groups, make sure you deselect this option before changing + the background colour.

      +

      + The "Colour→Colour Text..." + entry opens a dialog box to set a different text colour for light + and dark background, and the intensity threshold for transition + between them. +

      +

      The default colour schemes are summarised in the table below: +

      +

       

      +

      + Protein Colour Schemes +

      + + + + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      ARNDCQEGHILKMFPSTWYVBXZ
      Clustal
      Zappo
      Taylor
      Hydrophobicity
      Helix Propensity
      Strand Propensity
      Turn Propensity
      Buried Index
      +
      +

       

      +

      + Nucleotide Colour Schemes +

      + + + + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      ACGTUIXRYNWSMKBHDV
      Nucleotide
      Purine/Pyrimidine
      +
      -
      -

       

      +
      +

       

      diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html index 745b5a1..a31974f 100755 --- a/help/html/colourSchemes/nucleotide.html +++ b/help/html/colourSchemes/nucleotide.html @@ -19,7 +19,8 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Nucleotide Colour Scheme + +Nucleotide Colour Scheme -

      - Nucleic Acid Support -

      -

      - Colour Schemes -

      -

      Jalview has color schemes for nucleic acid based sequences, - ability to fetch sequences from RFAM and RNA secondary structure - coloring

      -

      - Information on the Nucleotide - colour scheme and - Purine/Pyrimidine colour scheme are available under the Colour Menu. - See Colour Schemes. -

      -

      - RNA Support -

      - Jalview supports annotation of RNA sequences with secondary structure - information. You can interactively - create and edit RNA - secondary structure annotation rows, or import data in the following - way: -
        -
      • RFAM - Sequences can be fetched from the RFAM database - by accession number or ID.
        • -
      • Stockholm files - WUSS (or VIENNA) dot-bracket - notation found in the secondary structure annotation line will be - imported as sequence or alignment associated secondary structure - annotation.
        • -
      • Clustal files - certain RNA alignment programs, such - as LocaRNA - output consensus RNA secondary structure lines in the line normally - reserved for the Clustal consensus line in a clustal file.
        • -
      • RNAML Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure
        • -
      -

      - RNA Secondary Structure Visualization and Analysis
      - If a sequence or RNA alignment has secondary structure information, - the alignment will have a secondary structure line shown below it, and - a number of additional options become available: -

        -
      • RNA - Helix colouring - highlights columns of alignment involved in - particular RNA helices, Uses the first displayed secondary structure annotation.
        • -
      • Base Pair - Conservation Analysis - shown as a histogram and base-pair logo - below the alignment. Uses the first displayed secondary structure annotation row.
        • -
      • 2D Structure - Visualization in VARNA - allows linked viewing of the consensus or - an individual sequence's structure. Accessed via the Sequence ID popup menu.
        • +

        + Nucleic Acid Support +

        +

        + Colour Schemes +

        +

        Jalview has color schemes for nucleic acid based sequences, + ability to fetch sequences from RFAM and RNA secondary structure + coloring

        +

        + Information on the Nucleotide + colour scheme and + Purine/Pyrimidine colour scheme are available under the Colour + Menu. See Colour Schemes. +

        +

        + RNA Support +

        + Jalview supports annotation of RNA sequences with secondary structure + information. You can interactively + create and edit RNA + secondary structure annotation rows, or import data in the following + way: +
          +
        • RFAM - Sequences can be fetched from the RFAM database by accession number or ID.
          • +
        • Stockholm files - WUSS (or VIENNA) dot-bracket + notation found in the secondary structure annotation line will be + imported as sequence or alignment associated secondary structure + annotation.
          • +
        • Clustal files - certain RNA alignment programs, + such as LocaRNA output consensus RNA secondary structure lines in the + line normally reserved for the Clustal consensus line in a clustal + file.
          • +
        • RNAML Jalview can import RNAML files containing + sequences and extended secondary structure annotation derived from + RNA 3D structure
          • +
        +

        + RNA Secondary Structure Visualization and Analysis
        + If a sequence or RNA alignment has secondary structure information, + the alignment will have a secondary structure line shown below it, + and a number of additional options become available: +

          +
        • RNA + Helix colouring - highlights columns of alignment involved in + particular RNA helices, Uses the first displayed secondary + structure annotation.
          • +
        • Base + Pair Conservation Analysis - shown as a histogram and base-pair + logo below the alignment. Uses the first displayed secondary + structure annotation row.
          • +
        • 2D Structure + Visualization in VARNA - allows linked viewing of the consensus + or an individual sequence's structure. Accessed via the Sequence + ID popup menu.
        • per sequence secondary structure annotation
          Sequence associated secondary structure annotation imported via stockholm, PDB files, or other sources can @@ -95,15 +102,23 @@ td { Annotation→Secondary Structure option (only present when per-sequence secondary structure is available).
        -

        Pseudo-knots
        - Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.
        - Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.

        - -

        Limitations when working with RNA in Jalview
        - Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation -
        - Jalview's RNA handling capabilities were introduced in v2.8 -

        -

         

        +

        + Pseudo-knots
        Jalview 2.8.2 introduced limited + support for working with structures including pseudoknots. Where + possible, extended WUSS symbols (e.g. different types of + parentheses, or upper and lower case letters) are preserved when + parsing RNA structure annotation and will be shaded differently when + displayed in the structure.
        Extended WUSS annotation is also + employed to distinguish different base pair interactions obtained + from RNAML files. +

        + +

        + Limitations when working with RNA in Jalview
        + Currently, Jalview is not able to export RNA secondary structure + annotation in any format other than Jalview annotation
        Jalview's + RNA handling capabilities were introduced in v2.8 +

        +

         

        diff --git a/help/html/privacy.html b/help/html/privacy.html index 858aa32..5c6939a 100644 --- a/help/html/privacy.html +++ b/help/html/privacy.html @@ -23,57 +23,65 @@ Jalview Privacy Statement -

        Privacy for Jalview Users
        -

        The Jalview Desktop application which is available from the -www.jalview.org site does not contain code designed to collect personal or -private information without your consent. However, we do collect usage -statistics to work out who is using Jalview, so we can apply for funding -to support Jalview development, and make it better for our users.

        -

        Usage data is collected from the logs of various web services that the Jalview Desktop contacts through its normal operation. -These are described below:

        -
          -
        • HTTP logs on the Jalview website
          - We record IP addresses of machines which access the web site, either - via the browser when downloading the application, or when the Jalview - Desktop user interface is launched.

          -
            -
          • The JNLP file at www.jalview.org/webstart/jalview.jnlp - is retrieved to determine if you are running the latest version of - Jalview.
            • -
          • The questionnaire web service at - www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique - cookie for the current questionnaire is stored in the Jalview - properties file.
            • -
          • The Jalview web services stack is contacted to - retrieve the currently available web services. All interactions with - the public Jalview web services are logged, but we delete all job data - (input data and results) after about two weeks.
            • -

          -
          • -
        • Google Analytics
          - Since Jalview 2.4.0b2, the Jalview Desktop records usage data with - Google Analytics via the JGoogleAnalytics - class.
          - The Google Analytics logs for Jalview version 2.4 only record the fact - that the application was started, but in the future, we will use this - mechanism to improve the Desktop user interface, by tracking which - parts of the user interface are being used most often.
          • -
        -

        -

        Stopping Jalview from calling home
        -If you run Jalview in 'headless mode' via the command line, then the -program shouldn't try to contact any of the web servers mentioned above -(if it does, then it's a bug!). You can also specify some command line options to disable -the questionnaire and usage statistics check. Finally, the Connections Tab of the -Jalview preferences contains options for controlling the submission of -usage statistics. -

        Other Web Clients in Jalview
        -The Jalview desktop is intended to make it easier to interact with -web-based bioinformatics resources. However, we can't take any -responsibility for the integrity of any external services you might -access via the program. Sorry!

        +

        + Privacy for Jalview Users
        +

        The Jalview Desktop application which is available from the + www.jalview.org site does not contain code designed to collect + personal or private information without your consent. However, we do + collect usage statistics to work out who is using Jalview, so we can + apply for funding to support Jalview development, and make it better + for our users.

        +

        Usage data is collected from the logs of various web services + that the Jalview Desktop contacts through its normal operation. + These are described below:

        +
          +
        • HTTP logs on the Jalview website
          We + record IP addresses of machines which access the web site, either + via the browser when downloading the application, or when the + Jalview Desktop user interface is launched.
          +
          +
            +
          • The JNLP file at + www.jalview.org/webstart/jalview.jnlp is retrieved to + determine if you are running the latest version of Jalview.
            • +
          • The questionnaire web service at + www.jalview.org/cgi-bin/questionnaire.pl is checked and a + unique cookie for the current questionnaire is stored in the + Jalview properties file.
            • +
          • The Jalview web services stack is contacted to + retrieve the currently available web services. All + interactions with the public Jalview web services are + logged, but we delete all job data (input data and results) + after about two weeks.
            • +
          +
          • +
        • Google Analytics
          Since Jalview 2.4.0b2, + the Jalview Desktop records usage data with Google Analytics via + the JGoogleAnalytics + class.
          The Google Analytics logs for Jalview version 2.4 + only record the fact that the application was started, but in the + future, we will use this mechanism to improve the Desktop user + interface, by tracking which parts of the user interface are being + used most often.
          • +
        +

        +

        + Stopping Jalview from calling home
        If you + run Jalview in 'headless mode' via the command line, then the + program shouldn't try to contact any of the web servers mentioned + above (if it does, then it's a bug!). You can also specify some command line options to disable the questionnaire and usage + statistics check. Finally, the Connections Tab of the Jalview preferences contains options for + controlling the submission of usage statistics. +

        + Other Web Clients in Jalview
        The Jalview + desktop is intended to make it easier to interact with web-based + bioinformatics resources. However, we can't take any responsibility + for the integrity of any external services you might access via the + program. Sorry! +

        diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index 292b2b6..73090d0 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -23,117 +23,136 @@ VAMSAS Interoperation -

        VAMSAS Interoperation

        -

        Jalview can interact with other applications using "the VAMSAS -Interoperation framework" which is an experimental model for -interoperation between bioinformatics applications (Visualization -and Analysis of Molecular Sequences, -Alignements and Structures). -Currently, the only other VAMSAS enabled application is TOPALi - a user friendly program for -phylogenetics and evolutionary analysis. -

        VAMSAS enabled applications access a shared bioinformatics -dataset containing sequences, alignments, annotation and trees, which -can be represented by an XML document analogous to a Jalview Project Archive.

        -
        -Connecting to a VAMSAS session
        -The VAMSAS functionality in Jalview is accessed through the Desktop's Vamsas -menu. The options available in this menu depend on whether the -application is currently interacting with a VAMSAS dataset in a VAMSAS -session. When the application is not connected to a session is active, -the menu options are as follows:
        -
          -
        • Connect to an existing session
          - If visible, this submenu contains a list of existing sessions that the - VAMSAS framework has discovered on your computer.
          - Choose one to connect to it.
          • -
        • New VAMSAS Session
          - This option will create a new session on your computer.
          • -
        • Load VAMSAS Session...
          - This option will open a file browser window allowing you to select a - VAMSAS session archive from which a new session will be created.
          - New in 2.5:Sessions created from an imported document inherit - the file or URL for the document.
          • +

          + VAMSAS Interoperation +

          +

          + Jalview can interact with other applications using "the VAMSAS + Interoperation framework" which is an experimental model for + interoperation between bioinformatics applications (Visualization + and Analysis of Molecular Sequences, + Alignements and Structures). + Currently, the only other VAMSAS enabled application is TOPALi - a user friendly program for phylogenetics and + evolutionary analysis. +

          + VAMSAS enabled applications access a shared bioinformatics dataset + containing sequences, alignments, annotation and trees, which can be + represented by an XML document analogous to a Jalview Project Archive. +

          +
          + Connecting to a VAMSAS session +
          The VAMSAS functionality in Jalview is accessed through the + Desktop's + Vamsas menu. The options available in this menu + depend on whether the application is currently interacting with a + VAMSAS dataset in a + VAMSAS session. When the application is not connected + to a session is active, the menu options are as follows: +
          +
            +
          • Connect to an existing session
            If + visible, this submenu contains a list of existing sessions that + the VAMSAS framework has discovered on your computer.
            + Choose one to connect to it.
            • +
          • New VAMSAS Session
            This option will + create a new session on your computer.
            • +
          • Load VAMSAS Session...
            This option will + open a file browser window allowing you to select a VAMSAS session + archive from which a new session will be created.
            New + in 2.5:Sessions created from an imported document inherit the + file or URL for the document.
            • -
          -
          -VAMSAS and Firewalls: VAMSAS uses sockets to -communicate between different programs. This means that after starting a -session, your firewall software may ask you whether to allow the java -executable access to the internet (port 53782). If you do not allow -this, messages will not be exchanged with other VAMSAS applications.
          -
          -Once you have successfully connected to a VAMSAS session, any data made -available by other VAMSAS applications will be automatically imported -into Jalview. However, in order to share the data in Jalview with other -VAMSAS applications, you must manually select the Vamsas→"Session -Update" entry that is visible when a session is active. Selecting -this option will update the VAMSAS session document, with the data -loaded into Jalview. Any new alignments, trees and annotation will be -written to the session, in addition to any edits you have made to data -originally stored in the document.
          -Saving the current session
          -You can save the current session as a VAMSAS Session archive using the Vamsas→"Session -Update". The file contains a snapshot of the current VAMSAS -session, including data from any other applications connected to the -session. Leaving a VAMSAS session
          -A session can be disconnected from at any time using the Vamsas→"Stop -Session" option. Selecting this option will only disconnect Jalview -from the session - any other applications will remain connected to the -session. If Jalview is the only application connected to the session and -you have not yet saved the VAMSAS session then you will be prompted with -an optional 'Save VAMSAS session...' dialog box, allowing the session to -be saved and returned to at a later date.
          -VAMSAS Session Persistence
          -VAMSAS sessions are persistent - this means that they exist -independently of any VAMSAS applications that are connected to them. -This means that if something goes wrong with a VAMSAS application and it -crashes or otherwise fails, the VAMSAS session it is connected to will -(hopefully) be unaffected. For instance, if Jalview is killed or crashes -whilst it is still connected to a session, that session can be recovered -in a new Jalview instance using the Vamsas→"Existing -session" sub menu.

          -

          A quick Demo -
          -Jalview can talk to itself through VAMSAS. Simply start two copies of -the application, create a new vamsas session in one, and connect to the -new session in the other. Then load your data into one of the -applications, and use the -Vamsas→"Session Update" -menu entry to try to propagate the data to the other application. -
          - - - - - - - - - - - - - - - - - - - - - -
          Data Sharing CapabilityJalview Version
          Alignments, sequences and annotation, trees, database - references, cDNA/protein mappings.2.4
          Mouseover location across linked DNA, protein and structure - positions.2.4
          Jalview project settings (Multiple views, groups, tree - partitions, colouring, window positions)2.5
          Sequence region and column selections2.5
          -
          -

          Version 0.2 of the VAMSAS client library is used in Jalview -2.5. For further details about the VAMSAS framework, please check the -VAMSAS website. The VAMSAS -framework is implemented as a Java 1.4 Library and depends on a number -of other open source projects. Its source is released under the -LGPL license.  

          +
        +
        + VAMSAS and Firewalls: VAMSAS uses sockets to + communicate between different programs. This means that after starting + a session, your firewall software may ask you whether to allow the + java executable access to the internet (port 53782). If you do not + allow this, messages will not be exchanged with other VAMSAS + applications. +
        +
        Once you have successfully connected to a VAMSAS session, + any data made available by other VAMSAS applications will be + automatically imported into Jalview. However, in order to share the + data in Jalview with other VAMSAS applications, you must manually + select the + Vamsas→"Session Update" entry that is + visible when a session is active. Selecting this option will update + the VAMSAS session document, with the data loaded into Jalview. Any + new alignments, trees and annotation will be written to the session, + in addition to any edits you have made to data originally stored in + the document. +
        + Saving the current session +
        You can save the current session as a VAMSAS Session archive + using the + Vamsas→"Session Update". The file + contains a snapshot of the current VAMSAS session, including data from + any other applications connected to the session. + Leaving a VAMSAS session +
        A session can be disconnected from at any time using the + Vamsas→"Stop Session" option. + Selecting this option will only disconnect Jalview from the session - + any other applications will remain connected to the session. If + Jalview is the only application connected to the session and you have + not yet saved the VAMSAS session then you will be prompted with an + optional 'Save VAMSAS session...' dialog box, allowing the session to + be saved and returned to at a later date. +
        + VAMSAS Session Persistence +
        VAMSAS sessions are persistent - this means that they exist + independently of any VAMSAS applications that are connected to them. + This means that if something goes wrong with a VAMSAS application and + it crashes or otherwise fails, the VAMSAS session it is connected to + will (hopefully) be unaffected. For instance, if Jalview is killed or + crashes whilst it is still connected to a session, that session can be + recovered in a new Jalview instance using the + Vamsas→"Existing session" sub menu. +

        +

        + A quick Demo
        Jalview can talk to itself + through VAMSAS. Simply start two copies of the application, create a + new vamsas session in one, and connect to the new session in the + other. Then load your data into one of the applications, and use the + Vamsas→"Session Update" menu entry + to try to propagate the data to the other application.
        + + + + + + + + + + + + + + + + + + + + + +
        Data Sharing CapabilityJalview Version
        Alignments, sequences and annotation, trees, database + references, cDNA/protein mappings.2.4
        Mouseover location across linked DNA, protein and + structure positions.2.4
        Jalview project settings (Multiple views, groups, tree + partitions, colouring, window positions)2.5
        Sequence region and column selections2.5
        +
        +

        + Version 0.2 of the VAMSAS client library is used in Jalview + 2.5. For further details about the VAMSAS framework, please check + the VAMSAS website. The VAMSAS + framework is implemented as a Java 1.4 Library and depends on a + number of other open source projects. Its source is released under + the LGPL license.   +

        diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html index 6c1e7ec..5dd4472 100644 --- a/help/html/webServices/AACon.html +++ b/help/html/webServices/AACon.html @@ -23,50 +23,52 @@ AACon Web Service - AACon Alignment Conservation Calculation Service -

        The JABAWS AACon service implements 17 different conservation - scores for protein sequence alignments.

        -

        - The majority of these scores were described by Valdar in 2002 (Scoring - residue conservation. Proteins: Structure, Function, and - Genetics 43(2): 227-241. PubMed or - available on the Valdar - Group publications page), but the SMERFs score was developed later - and described by Manning et al. in 2008 (BMC - Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51). -

        -

        - Enabling and disabling AACon calculations
        When - the AACon Calculation entry in the Web - Services→Conservation is ticked, AACon calculations will be - performed every time the alignment is modified. Selecting the menu - item will enable or disable automatic recalculation. -

        -

        - Configuring which AACon calculations are performed
        - The Web Services→Conservation→Change AACon - Settings ... menu entry will open a web - services parameter dialog for the currently configured AACon server. - Standard presets are provided for quick and more expensive - conservation calculations, and parameters are also provided to change - the way that SMERFS calculations are performed.
        AACon - settings for an alignment are saved in Jalview projects along with - the latest calculation results. - -

        -

        - Changing the server used for AACon calculations
        - If you are working with alignments too large to analyse with the - public JABAWS server, then you will most likely have already - configured additional JABAWS - servers. By default, Jalview will chose the first AACon service - available from the list of JABAWS servers available. If available, you can switch to - use another AACon service by selecting it from the Web - Services→Conservation→Switch Server submenu. -

        + AACon Alignment Conservation Calculation Service +

        The JABAWS AACon service implements 17 different conservation + scores for protein sequence alignments.

        +

        + The majority of these scores were described by Valdar in 2002 + (Scoring residue conservation. Proteins: Structure, + Function, and Genetics 43(2): 227-241. PubMed or available on the Valdar Group publications page), but the SMERFs score was + developed later and described by Manning et al. in 2008 (BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51). +

        +

        + Enabling and disabling AACon calculations
        + When the AACon Calculation entry in the Web + Services→Conservation is ticked, AACon calculations will be + performed every time the alignment is modified. Selecting the menu + item will enable or disable automatic recalculation. +

        +

        + Configuring which AACon calculations are performed
        + The Web Services→Conservation→Change + AACon Settings ... menu entry will open a web services parameter dialog for the currently configured AACon + server. Standard presets are provided for quick and more expensive + conservation calculations, and parameters are also provided to + change the way that SMERFS calculations are performed.
        AACon + settings for an alignment are saved in Jalview projects along with the latest calculation results. + +

        +

        + Changing the server used for AACon calculations
        + If you are working with alignments too large to analyse with the + public JABAWS server, then you will most likely have already + configured additional JABAWS + servers. By default, Jalview will chose the first AACon service + available from the list of JABAWS servers available. If available, + you can switch to use another AACon service by selecting it from the + Web Services→Conservation→Switch Server + submenu. +

        diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html index 6a6921e..6750b55 100644 --- a/help/html/webServices/JABAWS.html +++ b/help/html/webServices/JABAWS.html @@ -23,44 +23,59 @@ The JABAWS system -

        The JAva Bioinformatics -Analysis Web Services -system (JABAWS)
        -Jalview includes a client for interacting with programmatic (SOAP) web -services for the JABAWS -service model, developed at the University of Dundee by Peter Troshin -and Geoff Barton. This is an open source system that provides a -framework for wrapping command line bioinformatics analysis programs -that enables them to be executed locally or on a cluster using data and -analysis parameters provided by a program linked with the JABA engine directly or -accessing it remotely via its web services interface.

        -

        The list of JABAWS servers known to the Jalview desktop is shown -in the Web Services Preferences -Panel, and detailed information about a particular service is available -from the help text and web pages accessible from its job parameters dialog box.

        -

        Obtaining JABAWS
        -One of the aims of JABAWS is to enable you to easily perform -computationally intensive bioinformatics analysis tasks using your own -computational facilities. It can be installed on a workstation to -provide stand-alone execution of analysis programs, or as a job -submission engine - enabling larger numbers of jobs to be handled. If -you would like to download and install JABAWS for your own use, please -go to http://www.compbio.dundee.ac.uk/jabaws -for more information.

        -

        Configuring your own JABAWS services for use by -Jalview
        -Once you have downloaded and installed JABAWS, and verified it is -working, all that is needed is to add the URL for your JABAWS server(s) to -the list in the Web Services -Preferences Panel. After adding your service and saving your preferences -or hitting the 'refresh web services' button, you should be able to -submit jobs to the server via the alignment window's web services menu. -Your JABAWS servers list is stored in your Jalview preferences, so you -will only have to configure Jalview once for each new server.

        -

        Support for accessing JABAWS servers was introduced in -Jalview 2.6.

        -

        Option for adding JABAWS servers which fails validation -was introduced from version 2.8.2

        +

        + The JAva Bioinformatics + Analysis Web Services + system (JABAWS)
        Jalview + includes a client for interacting with programmatic (SOAP) web + services for the JABAWS + service model, developed at the University of Dundee by Peter + Troshin and Geoff Barton. This is an open source system that + provides a framework for wrapping command line bioinformatics + analysis programs that enables them to be executed locally or on a + cluster using data and analysis parameters provided by a program + linked with the JABA engine directly or accessing it remotely via + its web services interface. +

        +

        + The list of JABAWS servers known to the Jalview desktop is shown in + the Web Services Preferences + Panel, and detailed information about a particular service is + available from the help text and web pages accessible from its job parameters dialog box. +

        +

        + Obtaining JABAWS
        One of the aims of JABAWS + is to enable you to easily perform computationally intensive + bioinformatics analysis tasks using your own computational + facilities. It can be installed on a workstation to provide + stand-alone execution of analysis programs, or as a job submission + engine - enabling larger numbers of jobs to be handled. If you would + like to download and install JABAWS for your own use, please go to http://www.compbio.dundee.ac.uk/jabaws for more information. +

        +

        + Configuring your own JABAWS services for use by + Jalview
        Once you have downloaded and installed JABAWS, + and verified it is working, all that is needed is to add the URL for + your JABAWS server(s) to the list in the Web Services Preferences Panel. After adding your service and + saving your preferences or hitting the 'refresh web services' + button, you should be able to submit jobs to the server via the + alignment window's web services menu. Your JABAWS servers list is + stored in your Jalview preferences, so you will only have to + configure Jalview once for each new server. +

        +

        + Support for accessing JABAWS servers was introduced in + Jalview 2.6. +

        +

        + Option for adding JABAWS servers which fails validation was + introduced from version 2.8.2 +

        diff --git a/help/html/webServices/RNAalifold.html b/help/html/webServices/RNAalifold.html index 461c720..432e0a6 100644 --- a/help/html/webServices/RNAalifold.html +++ b/help/html/webServices/RNAalifold.html @@ -25,62 +25,65 @@ RNAalifold Web Service - RNAalifold RNA Alignment Secondary Structure - Prediction Service -

        - RNAalifold analyses the pattern of base pair conservation in an RNA - alignment in order to predict a consensus secondary structure.
        It - is part of the Vienna - RNA Secondary Structure Prediction and Comparison Package. It was - described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R. - Gruber, and Peter F. Stadler, RNAalifold: Improved consensus - structure prediction for RNA alignments (BMC Bioinformatics, 9:474, - 2008). Download the paper at http://www.biomedcentral.com/1471-2105/9/474. -

        -

        - Running RNAalifold from Jalview
        -

        - Jalview supports access to RNAalifold services provided by JABA 2.1 - servers. To enable RNAalifold predictions for an RNA alignment, go to - Webservices→Secondary Structure Prediction and - select RNAalifold prediction to run with current - defaults, and Change settings ... to adjust - prediction parameters. The RNA secondary structure prediction for the - alignment will be shown as alignment annotation, and any edits will - trigger the prediction to be recalculated. -

        - RNAalifold prediction parameters
        JABAWS and - Jalview only provide access to a selection of the RNAalifold - arguments. For a full description, see the documentation at http://www.tbi.univie.ac.at/RNA/RNAalifold.html. -

        -

        - Supported Arguments which give alternate structures -

        -

        - Partition Function (-p)
        Calculate the Partition - Function and base pairing probability matrix in addition to the mfe - structure. A coarse representation of the pair probabilities in the - form of a pseudo bracket notation, as well as the centroid structure - derived from the pair probabilities are displayed. The most likely - base pairings are stored in a separate file by RNAalifold and - represented in Jalview by a bar graph annotation line labeled - 'Contact Probabilities'. -

        -

        - Maximum Expected Accuracy Structure (--MEA)
        Calculate - an MEA structure where the expected Accuracy is computed from the base - pair probabilities. A more detailed description can be found in the RNAfold - program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html. -

        -

        - Example RNAalifold Structure Annotation rows -

        -

        - -
        -

        + RNAalifold RNA Alignment Secondary Structure + Prediction Service +

        + RNAalifold analyses the pattern of base pair conservation in an RNA + alignment in order to predict a consensus secondary structure.
        It + is part of the Vienna + RNA Secondary Structure Prediction and Comparison Package. It was + described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R. + Gruber, and Peter F. Stadler, RNAalifold: Improved + consensus structure prediction for RNA alignments (BMC + Bioinformatics, 9:474, 2008). Download the paper at http://www.biomedcentral.com/1471-2105/9/474. +

        +

        + Running RNAalifold from Jalview
        +

        + Jalview supports access to RNAalifold services provided by JABA 2.1 + servers. To enable RNAalifold predictions for an RNA alignment, go + to Webservices→Secondary Structure Prediction + and select RNAalifold prediction to run with + current defaults, and Change settings ... to adjust + prediction parameters. The RNA secondary structure prediction for + the alignment will be shown as alignment annotation, and any edits + will trigger the prediction to be recalculated. +

        + RNAalifold prediction parameters
        JABAWS and + Jalview only provide access to a selection of the RNAalifold + arguments. For a full description, see the documentation at http://www.tbi.univie.ac.at/RNA/RNAalifold.html. +

        +

        + Supported Arguments which give alternate structures +

        +

        + Partition Function (-p)
        Calculate the Partition + Function and base pairing probability matrix in addition to the mfe + structure. A coarse representation of the pair probabilities in the + form of a pseudo bracket notation, as well as the centroid structure + derived from the pair probabilities are displayed. The most likely + base pairings are stored in a separate file by RNAalifold and + represented in Jalview by a bar graph annotation line labeled + 'Contact Probabilities'. +

        +

        + Maximum Expected Accuracy Structure (--MEA)
        + Calculate an MEA structure where the expected Accuracy is computed + from the base pair probabilities. A more detailed description can be + found in the RNAfold program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html. +

        +

        + Example RNAalifold Structure Annotation rows +

        +

        + +
        +

        diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html index 0840768..e919f3f 100644 --- a/help/html/webServices/dbreffetcher.html +++ b/help/html/webServices/dbreffetcher.html @@ -20,61 +20,78 @@ --> - -Database Reference Fetching +Database Reference Fetching

        -

        Discovering Database References for Sequences
        -Database references are associated with a sequence are displayed as a -list in the tooltip shown when mousing over its sequence ID. Jalview -uses references for the retrieval of PDB structures and DAS features, and for -retrieving sequence cross-references such as the protein products of a -DNA sequence.

        -

        Initiating reference retrieval
        -The application provides three ways to access the retrieval function. Either: -

        • select the Discover PDB IDs option from the structure submenu of the sequence's popup menu
          • -
        • Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's Web Services menu:
            -
          • Standard Databases will fetch references from the EBI databases plus currently selected DAS sources
            • -
          • The other entries submenus leading to lists of individual database sources that Jalview can access.
          • -
        • Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.
          • -
        +

        + Discovering Database References for Sequences
        + Database references are associated with a sequence are displayed as a + list in the tooltip shown when mousing over its sequence ID. Jalview + uses references for the retrieval of PDB structures and DAS + features, and for retrieving sequence cross-references such as the + protein products of a DNA sequence. +

        +

        + Initiating reference retrieval
        The + application provides three ways to access the retrieval function. + Either: +

          +
        • select the Discover PDB IDs option from the + structure submenu of the sequence's popup menu +
          • +
        • Choose one of the options from the 'Fetch DB Refs' submenu in + the alignment window's Web Services menu: +
            +
          • Standard Databases will fetch references from + the EBI databases plus currently selected DAS sources
            • +
          • The other entries submenus leading to lists of individual + database sources that Jalview can access.
            • +
          +
          • +
        • Answer 'Yes' when asked if you wish to retrieve database + references for your sequences after initiating a DAS Sequence + Feature fetch.
          • +

        Jalview discovers references for a sequence by generating a set -of ID queries from the ID string of each sequence in the alignment. It -then tries to query a subset of all the databases it can access in order to match -the alignment sequence to any records retrieved from the database. If a -match is found, then the sequence is annotated with that database's -reference, and any cross-references that its records contain.

        -

        The Sequence Identification Process
        -The method of accession id discovery is derived from the method which -earlier Jalview versions used for Uniprot sequence feature retrieval, -and was originally restricted to the identification of valid Uniprot -accessions.
        -Essentially, Jalview will try to retrieve records from a subset of the databases -accessible by the sequence -fetcher using each sequence's ID string (or each string in the ID -separated by the '∣' symbol).

        + of ID queries from the ID string of each sequence in the alignment. It + then tries to query a subset of all the databases it can access in + order to match the alignment sequence to any records retrieved from + the database. If a match is found, then the sequence is annotated with + that database's reference, and any cross-references that its records + contain.

        +

        + The Sequence Identification Process
        The + method of accession id discovery is derived from the method which + earlier Jalview versions used for Uniprot sequence feature retrieval, + and was originally restricted to the identification of valid Uniprot + accessions.
        Essentially, Jalview will try to retrieve records + from a subset of the databases accessible by the sequence fetcher using each sequence's ID string (or each string in + the ID separated by the '∣' symbol). +

        If a record (or set of records) is retrieved by any query derived -from the ID string of a sequence, then the sequence is aligned to the -ones retrieved to determine the correct start and end residue positions -(which are displayed when the 'Show Full Sequence ID' option). This is -important for the correct display of the location of any features -associated with that database.

        + from the ID string of a sequence, then the sequence is aligned to the + ones retrieved to determine the correct start and end residue + positions (which are displayed when the 'Show Full Sequence ID' + option). This is important for the correct display of the location of + any features associated with that database.

        If the alignment reveals differences between the sequence in the -alignment and the one in the record, then Jalview will assume that the -aligned sequence is not the one in the retrieved record.

        -

        In some cases, the ID used to retrieve records may be out -of date and a dialog box will be opened indicating that a 100% match -between the sequence and the record was identified, but the -sequence name is different. In this case, the can be manually -changed (by right clicking on the sequence ID and selecting Sequence→Edit -Name). + alignment and the one in the record, then Jalview will assume that the + aligned sequence is not the one in the retrieved record.

        +

        + In some cases, the ID used to retrieve records may be out of date and + a dialog box will be opened indicating that a 100% match between the + sequence and the record was identified, but the sequence name is + different. In this case, the can be manually changed (by right + clicking on the sequence ID and selecting Sequence→Edit + Name).

          -
        • Note
          - Please remember to save your alignment if either the start/end - numbering, or the sequence IDs were updated during the ID - retrieval process.
          • +
        • Note
          Please remember to save your alignment + if either the start/end numbering, or the sequence IDs were updated + during the ID retrieval process.
        diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index c4d1e8d..04ccd8f 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -23,63 +23,76 @@ Web Services -

        - Web services -

        +

        + Web services +

        -

        Jalview includes clients for a variety of web services for both - bioinformatic data retrieval and analysis. -

          -
        • The Sequence Fetcher - utilises web services for sequence, alignment and structure retrieval - provided by the European Bioinformatics Institute (EBI) and - Distributed Annotation System servers that are capable of serving - sequences.
          • -
        • The DAS Feature - Fetcher enables the retrieval and visualization of features from DAS - annotation sources
          • -
        • The Database Reference - Fetcher transfers database references from records available from - DAS or the public sequence databases.
          • -
        • The Web Services menu in each alignment - window also provides access to the following: - -

          - Web Service Dialog Box -

          -

          This dialog box is displayed when a web service job is - submitted. It gives the name of the service and any method citation - information, and monitors the progress of the calculation. The - cancel button will permanently cancel the job, but this is only - possible for some services.

          The Web - Services Preference panel controls the display and appearance of the - submission and analysis services in the Web Services - menu.
          • -
        • If Jalview encounters problems accessing any services, it may - display a warning - dialog box (this can be turned off using the web services - preferences tab).
          • -
        -

        -

        - More about Jalview's Web Services
        Jalview's - distributed computations utilise SOAP and REST - web services exposing sequence alignment, analysis, and secondary - structure prediction programs. Originally, Jalview 2's services were - maintained by the Barton group at the University of Dundee, and ran - programs on the Life Sciences High-performace Computing Cluster. With - the advent of JABAWS, - however, it is possible for anyone to host Jalview web services. -

        +

        Jalview includes clients for a variety of web services for both + bioinformatic data retrieval and analysis. +

          +
        • The Sequence + Fetcher utilises web services for sequence, alignment and + structure retrieval provided by the European Bioinformatics + Institute (EBI) and Distributed Annotation System servers that are + capable of serving sequences. +
          • +
        • The DAS Feature + Fetcher enables the retrieval and visualization of features from + DAS annotation sources +
          • +
        • The Database Reference + Fetcher transfers database references from records available + from DAS or the public sequence databases. +
          • +
        • The Web Services menu in each alignment + window also provides access to the following: + +

          + Web Service Dialog Box +

          +

          This dialog box is displayed when a web service job is + submitted. It gives the name of the service and any method + citation information, and monitors the progress of the + calculation. The cancel button will permanently cancel the job, + but this is only possible for some services.

          The Web Services Preference panel controls the display and appearance + of the submission and analysis services in the Web + Services menu. +
          • +
        • If Jalview encounters problems accessing any services, it + may display a warning + dialog box (this can be turned off using the web services + preferences tab). +
          • +
        +

        +

        + More about Jalview's Web Services
        + Jalview's distributed computations utilise SOAP and REST web services exposing sequence alignment, analysis, and + secondary structure prediction programs. Originally, Jalview 2's + services were maintained by the Barton group at the University of + Dundee, and ran programs on the Life Sciences High-performace + Computing Cluster. With the advent of JABAWS, however, it is possible for anyone to host Jalview web + services. +

        diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 0f64115..0dfbd10 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -23,8 +23,8 @@ JNet Secondary Structure Prediction -JNet Secondary Structure Prediction -

        + JNet Secondary Structure Prediction +

        Secondary structure prediction methods attempts to infer the likely secondary structure for a protein based on its amino acid composition and similarity to sequences with known secondary @@ -32,100 +32,108 @@ series of neural networks trained to predict different secondary structure types from a sequence profile, and when necessary, employs a jury network to identify the most likely secondary structure - prediction.

        • Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)
          -JPred4: a protein secondary structure prediction server
          -Nucleic Acids Research, Web Server issue (first published 15th April 2015)
          -http://dx.doi.org/10.1093/nar/gkv332 -
          • -
        • Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 - secondary structure prediction server Nucleic Acids Research 36 - W197-W201
          • -
        • Cuff J. A and Barton G.J (1999) Application of enhanced - multiple sequence alignment profiles to improve protein secondary - structure prediction Proteins 40 502-511
          • -
        -

        -The function available from the -Web Service→Secondary Structure -Prediction→JNet Secondary Structure Prediction -menu does two different kinds of prediction, dependent upon the -currently selected region: -

        -
          -
        • If nothing is selected, and the displayed sequences appear to - be aligned, then a JNet prediction will be run for the first sequence - in the alignment, using the current alignment. Otherwise the first - sequence will be submitted for prediction.
          • -
        • If just one sequence (or a region on one sequence) has been - selected, it will be submitted to the automatic JNet prediction server - for homolog detection and prediction.
          • -
        • If a set of sequences are selected, and they appear to be - aligned, then the alignment will be used for a Jnet prediction on the first - sequence selected in the set (that is, the one nearest the top of the - alignment window).
          • -
        -

        Note: JNet secondary structure prediction is a -'non-column-separable' service - predictions are based on the sequence -profile of contiguous stretches of amino-acid sequence. A prediction -will only be made on the visible parts of a sequence (see hiding columns) as if it were -a contiguous polypeptide chain. Prediction accuracy at the hidden column -boundaries may therefore be less than indicated by JNet's own -reliability score (see below).

        -

        The result of a JNet prediction for a sequence is a new annotated -alignment window:

        - -

        The sequence for which the prediction was made is the first one -in the alignment. If a sequence based prediction was made then the -remaining sequences in the alignment are the aligned parts of homologs -which were used to construct a sequence profile for the prediction. If -the prediction was made using a multiple alignment, then the original -multiple alignment will be returned, annotated with the prediction.

        -The annotation bars below the alignment are as follows: -

        -
          -
        • Lupas_21, Lupas_14, Lupas_28
          - Coiled-coil predictions for the sequence. These are binary - predictions for each location.
          • -
        • JNETSOL25,JNETSOL5,JNETSOL0
          - Solvent accessibility predictions - binary predictions of 25%, - 5% or 0% solvent accessibility.
          • -
        • JNetPRED
          - The consensus prediction - helices are marked as red tubes, - and sheets as dark green arrows.
          • -
        • JNetCONF
          - The confidence estimate for the prediction. High values mean - high confidence. prediction - helices are marked as red tubes, and - sheets as dark green arrows.
          • -
        • JNetALIGN
          - Alignment based prediction - helices are marked as red tubes, - and sheets as dark green arrows.
          • -
        • JNetHMM
          - HMM profile based prediction - helices are marked as red - tubes, and sheets as dark green arrows.
          • -
        • jpred
          - Jpred prediction - helices are marked as red tubes, and sheets - as dark green arrows.
          • -
        • JNETPSSM
          - PSSM based prediction - helices are marked as red tubes, and - sheets as dark green arrows.
          • -
        • JNETFREQ
          - Amino Acid frequency based prediction - helices are marked as - red tubes, and sheets as dark green arrows.
          • -
        • JNETJURY
          - A '*' in this annotation indicates that the JNETJURY was - invoked to rationalise significantly different primary predictions.
          • -
        -

        - JNet annotation created in Jalview 2.8.2 and later versions - can be displayed on other alignments via the Add reference - annotation Sequence ID popup menu option. - - As of Jalview 2.6, the Jnet service accessed accessed via the -'Secondary structure prediction' submenu should be considered a legacy -Jalview SOAP service, and will be replaced in the near future by a -JPred4 Rest service. + prediction.
        +
          +
        • Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)
          + JPred4: a protein secondary structure prediction server
          Nucleic + Acids Research, Web Server issue (first + published 15th April 2015)
          http://dx.doi.org/10.1093/nar/gkv332 +
          • +
        • Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 + secondary structure prediction server Nucleic Acids + Research 36 W197-W201 +
          • +
        • Cuff J. A and Barton G.J (1999) Application of enhanced + multiple sequence alignment profiles to improve protein secondary + structure prediction Proteins 40 502-511 +
          • +
        +

        + The function available from the + Web Service→Secondary Structure + Prediction→JNet Secondary Structure Prediction menu does two + different kinds of prediction, dependent upon the currently selected + region: +

        +
          +
        • If nothing is selected, and the displayed sequences appear + to be aligned, then a JNet prediction will be run for the first + sequence in the alignment, using the current alignment. Otherwise + the first sequence will be submitted for prediction.
          • +
        • If just one sequence (or a region on one sequence) has been + selected, it will be submitted to the automatic JNet prediction + server for homolog detection and prediction.
          • +
        • If a set of sequences are selected, and they appear to be + aligned, then the alignment will be used for a Jnet prediction on + the first sequence selected in the set (that is, + the one nearest the top of the alignment window). +
          • +
        +

        + Note: JNet secondary structure prediction is a + 'non-column-separable' service - predictions are based on the + sequence profile of contiguous stretches of amino-acid sequence. A + prediction will only be made on the visible parts of a sequence (see + hiding columns) as if + it were a contiguous polypeptide chain. Prediction accuracy at the + hidden column boundaries may therefore be less than indicated by + JNet's own reliability score (see below). +

        +

        The result of a JNet prediction for a sequence is a new + annotated alignment window:

        + +

        The sequence for which the prediction was made is the first one + in the alignment. If a sequence based prediction was made then the + remaining sequences in the alignment are the aligned parts of + homologs which were used to construct a sequence profile for the + prediction. If the prediction was made using a multiple alignment, + then the original multiple alignment will be returned, annotated + with the prediction.

        + The annotation bars below the alignment are as follows: +

        +
          +
        • Lupas_21, Lupas_14, Lupas_28
          Coiled-coil + predictions for the sequence. These are binary predictions for + each location.
          • +
        • JNETSOL25,JNETSOL5,JNETSOL0
          Solvent + accessibility predictions - binary predictions of 25%, 5% or 0% + solvent accessibility.
          • +
        • JNetPRED
          The consensus prediction - + helices are marked as red tubes, and sheets as dark green + arrows.
          • +
        • JNetCONF
          The confidence estimate for the + prediction. High values mean high confidence. prediction - + helices are marked as red tubes, and sheets as dark green + arrows.
          • +
        • JNetALIGN
          Alignment based prediction - + helices are marked as red tubes, and sheets as dark green + arrows.
          • +
        • JNetHMM
          HMM profile based prediction - + helices are marked as red tubes, and sheets as dark green + arrows.
          • +
        • jpred
          Jpred prediction - helices are + marked as red tubes, and sheets as dark green arrows.
          • +
        • JNETPSSM
          PSSM based prediction - helices + are marked as red tubes, and sheets as dark green arrows.
          • +
        • JNETFREQ
          Amino Acid frequency based + prediction - helices are marked as red tubes, and sheets as dark + green arrows.
          • +
        • JNETJURY
          A '*' in this annotation + indicates that the JNETJURY was invoked to rationalise + significantly different primary predictions.
          • +
        +

        + JNet annotation created in Jalview 2.8.2 and later versions + can be displayed on other alignments via the Add reference annotation Sequence ID popup menu option. + + As of Jalview 2.6, the Jnet service accessed accessed via the + 'Secondary structure prediction' submenu should be considered a + legacy Jalview SOAP service, and will be replaced in the near future + by a JPred4 Rest service. diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 6ba604f..b685576 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -23,56 +23,72 @@ Multiple Sequence Alignment Web Service -Multiple Sequence Alignment Web Services -

        - Multiple sequence alignment services are accessed from the Alignment - submenu of the Alignment Window's Web Service menu. - When an entry from one of these menus is selected, either the - currently selected residues, or the whole sequence set (if there is no - selection or only one sequence is selected) will be submitted for - multiple sequence alignment. -

        -

        There are two kinds of multiple sequence alignment operations -available: -

          -
        • alignment - where a new alignment is constructed from - the input
          • -
        • realignment - where any aligned sequences will be - used by the service to construct a profile based alignment of the - remaining unaligned sequences.
          • -
        - JABAWS Alignment services
        Most alignment services are - provided by the - JABAWS framework, which allows you to - customise the precise parameters used when running each alignment - prgoram. In addition to the 'Default settings', you may choose from a - range of alignment preset settings, or create your own using the - 'Edit Settings And Run ..' dialog - box. -

        -

        Alignment programs supported by JABAWS.
        Versions shown are those bundled with JABAWS 2.01 - if you are using a different server, check its home page to find out which versions are provided.

        -

        + Multiple Sequence Alignment Web Services +

        + Multiple sequence alignment services are accessed from the Alignment + submenu of the Alignment Window's Web Service menu. + When an entry from one of these menus is selected, either the + currently selected residues, or the whole sequence set (if there is + no selection or only one sequence is selected) will be submitted for + multiple sequence alignment. +

        +

        There are two kinds of multiple sequence alignment operations + available: +

          +
        • alignment - where a new alignment is constructed + from the input
          • +
        • realignment - where any aligned sequences will be + used by the service to construct a profile based alignment of the + remaining unaligned sequences.
          • +
        + JABAWS Alignment services +
        Most alignment services are provided by the + JABAWS framework, which allows you to + customise the precise parameters used when running each alignment + prgoram. In addition to the 'Default settings', you may choose from a + range of alignment preset settings, or create your own using the + 'Edit Settings And Run ..' dialog + box. +

        +

        + Alignment programs supported by JABAWS.
        Versions + shown are those bundled with JABAWS 2.01 - if you are using a + different server, check its home page to find out which versions are + provided. +

        +

        -

        Multiple Alignments of Sequences with hidden -columns
        -Multiple alignment services are 'column separable' analysis operations. -If the input contains hidden -columns then each visible segment of the input sequence set will be -submitted for alignment separately, and the results concatenated (with -the hidden regions preserved) once all alignment functions have -completed. Each sub-job's state is reported in its own tab: -

        -

        Multiple Multiple Sequence Alignment -sub jobs running at once -
        -

        -
        -

        +

        + Multiple Alignments of Sequences with hidden + columns
        Multiple alignment services are 'column + separable' analysis operations. If the input contains hidden columns then each visible segment of the input sequence + set will be submitted for alignment separately, and the results + concatenated (with the hidden regions preserved) once all alignment + functions have completed. Each sub-job's state is reported in its + own tab: +

        +

        + Multiple Multiple Sequence Alignment sub jobs + running at once +
        +

        +
        + +
        +

        diff --git a/help/html/webServices/newsreader.html b/help/html/webServices/newsreader.html index cb46eca..ee69290 100644 --- a/help/html/webServices/newsreader.html +++ b/help/html/webServices/newsreader.html @@ -22,27 +22,29 @@ Jalview Desktop RSS News Reader -

        - The Jalview Desktop RSS News Reader
        The - Jalview Desktop includes a built in news reader for the Jalview Desktop - News Channel. -

        +

        + The Jalview Desktop RSS News Reader
        The + Jalview Desktop includes a built in news reader for the Jalview Desktop News Channel. +

        -

        We will use the desktop news channel to keep you informed of - important updates relevant to users of the Jalview desktop, such as - web service outages and user community events.

        -

        The news reader will be launched automatically when you start - the Desktop if new items are available. Should you want to browse - older items, however, you can open it manually from the 'Jalview news - reader' option in the Desktop's 'Tools' menu.

        - Snapshot of the Jalview Desktop's RSS reader -

        - The Jalview news reader was introduced in Jalview - version 2.7. Its implementation is based on JSwingReader. -

        +

        We will use the desktop news channel to keep you informed of + important updates relevant to users of the Jalview desktop, such as + web service outages and user community events.

        +

        The news reader will be launched automatically when you start + the Desktop if new items are available. Should you want to browse + older items, however, you can open it manually from the 'Jalview + news reader' option in the Desktop's 'Tools' menu.

        + Snapshot of the Jalview Desktop's RSS reader +

        + The Jalview news reader was introduced in Jalview version 2.7. Its implementation is based on JSwingReader. +

        diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html index 1f53a87..57e6698 100644 --- a/help/html/webServices/proteinDisorder.html +++ b/help/html/webServices/proteinDisorder.html @@ -23,223 +23,231 @@ JABAWS Protein Disorder Prediction Services -

        - JABAWS Protein Disorder Prediction Services
        - The Web Services→Disorder menu in the alignment - window allows access to protein disorder prediction services provided - by the configured JABAWS - servers. Each service operates on sequences in the alignment or - currently selected region (since Jalview 2.8.0b1) to identify - regions likely to be unstructured or flexible, or alternately, fold to - form globular domains. -

        -

        - Predictor results include both sequence - features and sequence associated alignment annotation rows. - Features display is controlled from the Feature Settings dialog - box. Clicking on the ID for a disorder prediction annotation row will - highlight or select (if double clicked) the associated sequence for - that row. You can also use the Sequence Associated option in - the Colour By - Annotation dialog box to colour sequences according to the results of - predictors shown as annotation rows. -

        -

        JABAWS 2.0 provides four disorder predictors which are described - below:

        - -

        - DisEMBL - (Linding et al., 2003)
        DisEMBL is a set of machine-learning - based predictors trained to recognise disorder-related annotation - found on PDB structures. -

        - - - - - - - - - - - - - - - - - - - - - -
        NameAnnotation typeDescription
        COILSSequence Feature &
        Annotation Row -         		Predicts loops/coils according to DSSP definition[1].
        Features mark range(s) of residues - predicted as loops/coils, and annotation row gives raw value for - each residue. Value over 0.516 indicates loop/coil. -
        HOTLOOPSSequence Feature &
        Annotation Row -         		"Hot loops constitute a refined subset of COILS, - namely those loops with a high degree of mobility as determined from - Cα temperature factors (B factors). It follows that highly - dynamic loops should be considered protein disorder."
        - Features mark range(s) of residues predicted to be hot loops and - annotation row gives raw value for each residue. Values over 0.6 - indicates hot loop. -
        REMARK465Sequence Feature &
        Annotation Row -         		"Missing coordinates in X-ray structure as defined by - remark465 entries in PDB. Nonassigned electron densities most often - reflect intrinsic disorder, and have been used early on in disorder - prediction."
        Features gives range(s) of residues - predicted as disordered, and annotation row gives raw value for each - residue. Value over 0.1204 indicates disorder. -
        +

        + JABAWS Protein Disorder Prediction Services
        + The Web Services→Disorder menu in the + alignment window allows access to protein disorder prediction + services provided by the configured JABAWS servers. Each service operates on sequences in the + alignment or currently selected region (since Jalview + 2.8.0b1) to identify regions likely to be unstructured or + flexible, or alternately, fold to form globular domains. +

        +

        + Predictor results include both sequence features and sequence associated alignment annotation rows. Features display is controlled from + the Feature Settings + dialog box. Clicking on the ID for a disorder prediction annotation + row will highlight or select (if double clicked) the associated + sequence for that row. You can also use the Sequence + Associated option in the Colour By Annotation dialog box to colour sequences according to + the results of predictors shown as annotation rows. +

        +

        JABAWS 2.0 provides four disorder predictors which are + described below:

        + +

        + DisEMBL + (Linding et al., 2003)
        DisEMBL is a set of + machine-learning based predictors trained to recognise + disorder-related annotation found on PDB structures. +

        + + + + + + + + + + + + + + + + + + + + + +
        NameAnnotation typeDescription
        COILSSequence Feature &
        Annotation Row +         		Predicts loops/coils according to DSSP definition[1].
        Features mark range(s) of residues predicted as + loops/coils, and annotation row gives raw value for each + residue. Value over 0.516 indicates loop/coil. +
        HOTLOOPSSequence Feature &
        Annotation Row +         		"Hot loops constitute a refined subset of COILS, + namely those loops with a high degree of mobility as determined + from Cα temperature factors (B factors). It follows that + highly dynamic loops should be considered protein + disorder."
        Features mark range(s) of residues + predicted to be hot loops and annotation row gives raw value for + each residue. Values over 0.6 indicates hot loop. +
        REMARK465Sequence Feature &
        Annotation Row +         		"Missing coordinates in X-ray structure as defined + by remark465 entries in PDB. Nonassigned electron densities most + often reflect intrinsic disorder, and have been used early on in + disorder prediction."
        Features gives range(s) of + residues predicted as disordered, and annotation row gives raw + value for each residue. Value over 0.1204 indicates disorder. +
        -

        - [1]. DSSP Classification: α-helix (H), - 310-helix (G), β-strand (E) are ordered, and all other states - (β-bridge (B), β-turn (T), bend (S), π-helix (I), and - coil (C)) considered loops or coils. -

        +

        + [1]. DSSP Classification: α-helix + (H), 310-helix (G), β-strand (E) are ordered, and all other + states (β-bridge (B), β-turn (T), bend (S), π-helix + (I), and coil (C)) considered loops or coils. +

        -

        - RONN a.k.a. - Regional Order Neural Network
        This predictor employs an approach - known as the 'bio-basis' method to predict regions of disorder in - sequences based on their local similarity with a gold-standard set of - disordered protein sequences. It yields a set of disorder prediction - scores, which are shown as sequence annotation below the alignment. -

        - - - - - - - - - - - -
        NameAnnotation typeDescription
        JRonn[2]Annotation RowRONN score for each residue in the sequence. Scores above - 0.5 identify regions of the protein likely to be disordered.
        -

        - [2]. JRonn denotes the score for this server because JABAWS - runs a Java port of RONN developed by Peter Troshin and distributed - as part of Biojava 3 - -

        -

        - IUPred
        IUPred - employs an empirical model to estimate likely regions of disorder. - There are three different prediction types offered, each using - different parameters optimized for slightly different applications. It - provides raw scores based on two models for predicting regions of - 'long disorder' and 'short disorder'. A third predictor identifies - regions likely to form structured domains. -

        - - - - - - - - - - - - - - - - - - - - - -
        NameAnnotation typeDescription
        Long disorderAnnotation RowPrediction of context-independent global disorder that - encompasses at least 30 consecutive residues of predicted disorder. - Employs a 100 residue window for calculation.
        Values above 0.5 - indicates the residue is intrinsically disordered. -
        Short disorderAnnotation RowPredictor for short, (and probably) context-dependent, - disordered regions, such as missing residues in the X-ray structure - of an otherwise globular protein. Employs a 25 residue window for - calculation, and includes adjustment parameter for chain termini - which favors disorder prediction at the ends.
        Values above 0.5 - indicate short-range disorder. -
        Structured domainsSequence FeatureFeatures highlighting likely globular domains useful for - structure genomics investigation.
        Post-analysis of disordered - region profile to find continuous regions confidently predicted to - be ordered. Neighbouring regions close to each other are merged, - while regions shorter than the minimal domain size of at least 30 - residues are ignored. -
        -

        - GLOBPLOT
        Defines regions - of globularity or natively unstructured regions based on a running sum - of the propensity of residues to be structured or unstructured. The - propensity is calculated based on the probability of each amino acid - being observed within well defined regions of secondary structure or - within regions of random coil. The initial signal is smoothed with a - Savitzky-Golay filter, and its first order derivative computed. - Residues for which the first order derivative is positive are - designated as natively unstructured, whereas those with negative - values are structured.
        - - - - - - - - - - - - - - - - - - - - - - - - - -
        NameAnnotation typeDescription
        Disordered RegionSequence Feature
        Sequence features marking range(s) of residues with - positive dydx values (correspond to the #Disorder column from JABAWS - results)
        Globular Domain - Sequence FeaturePutative globular domains
        DydxAnnotation rowFirst order derivative of smoothed score. Values above 0 - indicates residue is disordered.
        Smoothed Score
        Raw Score -         		Annotation RowThe smoothed and raw scores used to create the differential - signal that indicates the presence of unstructured regions.
        These - are hidden by default, but can be shown by right-clicking on the - alignment annotation panel and selecting Show - hidden annotation - -
        -

        - Documentation and thresholds for the JABAWS Disorder - predictors adapted from a personal communication by Nancy Giang, - 2012. -

        +

        + RONN a.k.a. Regional Order Neural Network
        This + predictor employs an approach known as the 'bio-basis' method to + predict regions of disorder in sequences based on their local + similarity with a gold-standard set of disordered protein sequences. + It yields a set of disorder prediction scores, which are shown as + sequence annotation below the alignment. +

        + + + + + + + + + + + +
        NameAnnotation typeDescription
        JRonn[2]Annotation RowRONN score for each residue in the sequence. Scores above + 0.5 identify regions of the protein likely to be disordered.
        +

        + [2]. JRonn denotes the score for this server because JABAWS + runs a Java port of RONN developed by Peter Troshin and + distributed as part of Biojava + 3 + +

        +

        + IUPred
        IUPred employs an empirical model to estimate + likely regions of disorder. There are three different prediction + types offered, each using different parameters optimized for + slightly different applications. It provides raw scores based on two + models for predicting regions of 'long disorder' and 'short + disorder'. A third predictor identifies regions likely to form + structured domains. +

        + + + + + + + + + + + + + + + + + + + + + +
        NameAnnotation typeDescription
        Long disorderAnnotation RowPrediction of context-independent global disorder that + encompasses at least 30 consecutive residues of predicted + disorder. Employs a 100 residue window for calculation.
        Values + above 0.5 indicates the residue is intrinsically disordered. +
        Short disorderAnnotation RowPredictor for short, (and probably) context-dependent, + disordered regions, such as missing residues in the X-ray + structure of an otherwise globular protein. Employs a 25 residue + window for calculation, and includes adjustment parameter for + chain termini which favors disorder prediction at the ends.
        Values + above 0.5 indicate short-range disorder. +
        Structured domainsSequence FeatureFeatures highlighting likely globular domains useful for + structure genomics investigation.
        Post-analysis of + disordered region profile to find continuous regions confidently + predicted to be ordered. Neighbouring regions close to each + other are merged, while regions shorter than the minimal domain + size of at least 30 residues are ignored. +
        +

        + GLOBPLOT
        Defines regions of globularity or natively + unstructured regions based on a running sum of the propensity of + residues to be structured or unstructured. The propensity is + calculated based on the probability of each amino acid being + observed within well defined regions of secondary structure or + within regions of random coil. The initial signal is smoothed with a + Savitzky-Golay filter, and its first order derivative computed. + Residues for which the first order derivative is positive are + designated as natively unstructured, whereas those with negative + values are structured.
        + + + + + + + + + + + + + + + + + + + + + + + + + +
        NameAnnotation typeDescription
        Disordered RegionSequence Feature
        Sequence features marking range(s) of residues + with positive dydx values (correspond to the #Disorder column + from JABAWS results)
        Globular Domain + Sequence FeaturePutative globular domains
        DydxAnnotation rowFirst order derivative of smoothed score. Values above 0 + indicates residue is disordered.
        Smoothed Score
        Raw Score +         		Annotation RowThe smoothed and raw scores used to create the + differential signal that indicates the presence of unstructured + regions.
        These are hidden by default, but can be + shown by right-clicking on the alignment annotation panel and + selecting Show hidden annotation + +
        +

        + Documentation and thresholds for the JABAWS Disorder + predictors adapted from a personal communication by Nancy Giang, + 2012. +

        diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html index 28bd82e..29e2c1e 100755 --- a/help/html/webServices/shmr.html +++ b/help/html/webServices/shmr.html @@ -23,46 +23,52 @@ Multi-Group Sequence Harmony and Multi-Relief - Functional residue analysis with Sequence Harmony and - Multi-Relief -

        - The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (Brandt, Feenstra and Heringa, 2010) available - from the Analysis sub-menu of the alignment window's web - services menu provides a method for the identification of significant - patterns of sub-family variation amongst the columns of an - alignment. -

        -

        - Instructions for use
        The service requires a - protein sequence multiple alignment that has been sub-divided into - groups containing at least two non-identical protein sequences. An - easy way to create groups is to use the built-in neighbour-joining or UPGMA tree - routines to calculate a tree for the alignment, and then click on the - tree to subdivide the alignment. -

        -

        - The SHMR service operates on the currently selected visible region(s) - of the alignment. Once submitted, a job progress window will display - status information about your job, including a URL which allows you to - visit the status page on the - IBIVU SHMR server. -

        -

        When the job is complete, Jalview will automatically open a new - window containing the alignment and groups that were submitted for - analysis, with additional histograms added portraying the SHMR scores - for each column of the sub-grouped alignment.

        -

        - If you use this service in your work, please cite :
        Brandt, - B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting - functional specificity from sequence alignment. Nucleic - Acids Res. 38: W35-W40. (* joint first authors) -

        - Note: The Multi-Harmony service is implemented with a prototype of Jalview's RESTful - web service client introduced in Jalview 2.7. A few bugs remain in this prototype, which we intend to fixed in version 2.7.1. -

      -

      + Functional residue analysis with Sequence Harmony and + Multi-Relief +

      + The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or + SHMR) service (Brandt, Feenstra and Heringa, + 2010) available from the Analysis sub-menu of the + alignment window's web services menu provides a method for the + identification of significant patterns of sub-family + variation amongst the columns of an alignment. +

      +

      + Instructions for use
      The service requires + a protein sequence multiple alignment that has been sub-divided into + groups containing at least two non-identical protein sequences. An + easy way to create groups is to use the built-in neighbour-joining or UPGMA tree routines to calculate a tree for + the alignment, and then click on the tree to subdivide the + alignment. +

      +

      + The SHMR service operates on the currently selected visible + region(s) of the alignment. Once submitted, a job progress window + will display status information about your job, including a URL + which allows you to visit the status page on the IBIVU SHMR server. +

      +

      When the job is complete, Jalview will automatically open a new + window containing the alignment and groups that were submitted for + analysis, with additional histograms added portraying the SHMR + scores for each column of the sub-grouped alignment.

      +

      + If you use this service in your work, please cite :
      + Brandt, B.W.*, Feenstra, K.A*. and Heringa, J. + (2010) Multi-Harmony: detecting functional specificity from sequence + alignment. Nucleic Acids Res. 38: W35-W40. (* joint first authors) + +

      + Note: The Multi-Harmony service is + implemented with a prototype of Jalview's RESTful web service client + introduced in Jalview 2.7. A few bugs remain in this prototype, + which we intend to fixed in version 2.7.1. +

    +

    diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 27ec782..de0f8cd 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -19,74 +19,82 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> - -Opening URLs from Jalview +Opening URLs from Jalview -

    -

    Opening URLs from Jalview
    -Both the applet and the desktop application are able to open URLs as -'popups' in your web browser.
    -Double-clicking on the ID of a sequence will open the first URL that can -be generated from its sequence ID. This is often the SRS site, but you -can easily configure your own sequence URL links.

    -

    Other links for a sequence either derived from any other -configured URL links, or imported from the sequence's annotation, are -accessed by right clicking to open the sequence pop-up menu, and -selecting from the Links submenu.

    -

    Configuring URL Links -
    URL links are defined in the "Connections" tab of the Jalview desktop preferences, or -specified as applet -parameters.
    -By default the item "SRS" is added to this link menu. This -link will show a web page in your default browser with the selected -sequence id as part of the URL.
    -In the preferences dialog box, click new to add a new -link, and edit to modify an existing link, or delete -to remove it.
    -You can name the link, this will be displayed on a new menu item under -the "Link" menu when you right click on a sequence id.
    -The URL string must contain a token that can be replaced with a sequence -ID. The simplest token is "$SEQUENCE_ID$", which will be -replaced by the chosen sequence id when you click on it.

    -

    eg.
    -UniRef100 = -http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
    -Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
    -
    -Links will also be made for any database cross references associated -with the sequence where the database name exactly matches a URL link -name. In this case, the $SEQUENCE_ID$ string will be replaced with the -accession string for the database cross-reference, rather than the -sequence ID for the sequence (since Jalview 2.4).

    -

    Regular Expression Substitution
    -A url may contain a string of the form $SEQUENCE_ID=/regular -expression/=$. In this case, the regular expression will be applied to -the full sequence ID string and the resulting match will be inserted -into the URL. Groups of parentheses can be used to specify which regions -of the regular expression will be used to generate the URL: -

      -
    • Each top level parenthesis will yield a URL containing the - text matched within that parenthesis.
      • -
    • Regions matching sub-parentheses within a top-level - parenthesis will be concatenated to form the text inserted into the URL - for the top-level parenthesis.
      • - Please Note: -
        -
      • The regular expressions supported by Jalview are those - provided by the Stevesoft javaregex - package.
        • -
      • Some characters must be escaped when specifying them as a - match within a regular expression.
        • -
      -
      - Many Thanks to Bernd Brandt of the Free University of Amsterdam for - testing this new regular-expression expansion feature!       - -
    -

    -

    +

    +

    + Opening URLs from Jalview
    Both the applet + and the desktop application are able to open URLs as 'popups' in + your web browser.
    Double-clicking on the ID of a sequence + will open the first URL that can be generated from its sequence ID. + This is often the SRS site, but you can easily configure your own sequence URL links. +

    +

    + Other links for a sequence either derived from any other configured + URL links, or imported from the sequence's annotation, are accessed + by right clicking to open the sequence pop-up menu, and selecting + from the Links submenu. +

    +

    + Configuring URL Links
    URL + links are defined in the "Connections" tab of the Jalview desktop preferences, or specified as applet parameters.
    By default the item "SRS" + is added to this link menu. This link will show a web page in your + default browser with the selected sequence id as part of the URL.
    + In the preferences dialog box, click new to add a + new link, and edit to modify an existing link, or delete + to remove it.
    You can name the link, this will be displayed + on a new menu item under the "Link" menu when you right + click on a sequence id.
    The URL string must contain a + token that can be replaced with a sequence ID. The simplest token is + "$SEQUENCE_ID$", which will be replaced by the chosen + sequence id when you click on it. +

    +

    + eg.
    UniRef100 = + http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
    + Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

    + Links will also be made for any database cross references associated + with the sequence where the database name exactly matches a URL link + name. In this case, the $SEQUENCE_ID$ string will be replaced with + the accession string for the database cross-reference, rather than + the sequence ID for the sequence (since Jalview 2.4). +

    +

    + Regular Expression Substitution
    A url may + contain a string of the form $SEQUENCE_ID=/regular + expression/=$. In this case, the regular expression will be + applied to the full sequence ID string and the resulting match will + be inserted into the URL. Groups of parentheses can be used to + specify which regions of the regular expression will be used to + generate the URL: +

      +
    • Each top level parenthesis will yield a URL containing the + text matched within that parenthesis.
      • +
    • Regions matching sub-parentheses within a top-level + parenthesis will be concatenated to form the text inserted into + the URL for the top-level parenthesis.
      • + Please Note: +
        +
      • The regular expressions supported by Jalview are those + provided by the Stevesoft + javaregex package. +
        • +
      • Some characters must be escaped when specifying them as + a match within a regular expression.
        • +

      Many Thanks to Bernd Brandt of the Free University of + Amsterdam for testing this new regular-expression expansion + feature! +       + +
    +

    +

    diff --git a/help/html/webServices/webServicesParams.html b/help/html/webServices/webServicesParams.html index dbff597..585cdfb 100644 --- a/help/html/webServices/webServicesParams.html +++ b/help/html/webServices/webServicesParams.html @@ -23,66 +23,80 @@ Web Service Job Parameter Dialog Box -

    Web service Job Parameter Dialog box

    +

    + Web service Job Parameter Dialog box +

    -

    Some Jalview services, including those provided by JABAWS, support a range of parameters and -options, enabling you to employ the most appropriate settings for the -input data. In addition to any preset combinations provided by -services themselves, the Web services parameters dialog box also allows -you to create and store your own parameter sets, so they can be accessed -quickly from the presets menu.

    -

    Accessing the parameter dialog box
    -The parameters dialog box is opened by selecting the 'Edit and Run' menu -entries within the JABAWS analysis submenu of the alignment window's web -services menu. Once opened, it presents the parameters and options -available for the chosen analysis for you to modify, and and also -enables you to browse any available service presets and select, create -or modify your own user defined parameter sets. Once you are satisfied -with the analysis parameters, press the Start Job -button to initiate the analysis.

    -

    Getting help on the analysis parameters
    -Each option or parameter shown in the dialog is accompanied by a brief -description, which is shown as a tooltip when the mouse is moved over -it. For some, a link symbol will also be shown (as in the example -below), indicating that further information is available online. In this -case, right-clicking (or command-click) will open a pop-up menu allowing -you to select a URL to open in your web browser.

    -

    -

    Analysis Parameters Dialog Box for JABAWS Services -
    -Parameter settings dialog box for JABAWS MAFFT Service
    -

    -

    The menu and text box at the top of the dialog box displays the -name of the current parameter set. The name can be edited, should you -wish to change or create a new user defined set, or clicked to present a -menu enabling other sets to be browsed. The description shown below may -also be edited (and the box resized to facilitate this), allowing you to -provide notes to accompany the parameter set. The modification of these -or any of the option or parameter settings will enable one or more of -the following buttons, that allow you to: -

      -
    • Revert the changes you have made. This will undo any - changes you have made to the parameters and options with respect to the - currently selected parameter set, reverting each setting to its default - or last saved value.
      • -
    • Create a new parameter set. Selecting this option - will create a new parameter set with the given name. New parameter sets - will be saved for the current session, but a file chooser will also - open which gives you the option to save the set for use in future - sessions.
      • -
    • Update an existing user defined parameter set. This - button will save any modifications you have made to the current - parameter set.
      • -
    • Rename the current user defined parameter set. This - will update the name recorded for the current parameter set.
      • -
    • Delete the current parameter set. Selecting this will - erase the current user defined parameter set from memory, and delete - its associated parameter file (if it exists).
      • -
    -

    -

    Support for adjusting and saving web service parameter -sets was added in Jalview 2.6

    +

    + Some Jalview services, including those provided by JABAWS, support a range of parameters and options, enabling you + to employ the most appropriate settings for the input data. In + addition to any preset combinations provided by services themselves, + the Web services parameters dialog box also allows you to create and + store your own parameter sets, so they can be accessed quickly from + the presets menu. +

    +

    + Accessing the parameter dialog box
    The + parameters dialog box is opened by selecting the 'Edit and Run' menu + entries within the JABAWS analysis submenu of the alignment window's + web services menu. Once opened, it presents the parameters and + options available for the chosen analysis for you to modify, and and + also enables you to browse any available service presets and select, + create or modify your own user defined parameter sets. Once you are + satisfied with the analysis parameters, press the Start + Job button to initiate the analysis. +

    +

    + Getting help on the analysis parameters
    + Each option or parameter shown in the dialog is accompanied by a + brief description, which is shown as a tooltip when the mouse is + moved over it. For some, a link symbol will also be shown (as in the + example below), indicating that further information is available + online. In this case, right-clicking (or command-click) will open a + pop-up menu allowing you to select a URL to open in your web + browser. +

    +

    +

    + Analysis Parameters Dialog Box for JABAWS Services
    Parameter settings dialog box for JABAWS MAFFT Service +
    +

    +

    The menu and text box at the top of the dialog box displays the + name of the current parameter set. The name can be edited, should + you wish to change or create a new user defined set, or clicked to + present a menu enabling other sets to be browsed. The description + shown below may also be edited (and the box resized to facilitate + this), allowing you to provide notes to accompany the parameter set. + The modification of these or any of the option or parameter settings + will enable one or more of the following buttons, that allow you to: + +

      +
    • Revert the changes you have made. This will undo + any changes you have made to the parameters and options with + respect to the currently selected parameter set, reverting each + setting to its default or last saved value.
      • +
    • Create a new parameter set. Selecting this option + will create a new parameter set with the given name. New parameter + sets will be saved for the current session, but a file chooser + will also open which gives you the option to save the set for use + in future sessions.
      • +
    • Update an existing user defined parameter set. + This button will save any modifications you have made to the + current parameter set.
      • +
    • Rename the current user defined parameter set. + This will update the name recorded for the current parameter set.
      • +
    • Delete the current parameter set. Selecting this + will erase the current user defined parameter set from memory, and + delete its associated parameter file (if it exists).
      • +
    +

    +

    + Support for adjusting and saving web service parameter sets + was added in Jalview 2.6 +

    diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html index 9f4c639..1950058 100644 --- a/help/html/webServices/webServicesPrefs.html +++ b/help/html/webServices/webServicesPrefs.html @@ -23,66 +23,83 @@ The Web Services Preferences Dialog Box -

    The Web Services Preferences Dialog Box

    +

    + The Web Services Preferences Dialog Box +

    -

    Jalview includes a range of web services clients for data -retrieval and analysis. The Web Services menu found in each -alignment window provides access to some of these services, and is -configured via the web services preference dialog box, -available from the Preferences panel from the Tools→Preferences... -menu from the Jalview Desktop window's menu bar.

    -

    -

    Web Services Preferences Panel
    -Web Services Preference Panel
    -

    -

    - Configuring the list of JABAWS servers
    The - main area of the panel shows the list of JABAWS - servers that Jalview is currently aware of. The list includes a colour coded status: - green indicates that all services are available for a given server, - amber signifies that one or more services on the server are not fully - functional, and red highlights servers that could not be contacted or - are not functional for some other reason. -

    -

    A server's URL may be added, -edited by double clicking on it, or deleted by selecting it and using -the buttons below. After adding or editing a server's URL, you will be -asked if you wish to test the server. If you wish to do so, then first -ensure you can view the new server's test report, which will be output -on Jalview's standard console output (you can open Jalview's built in -console viewer via the Tools→Java Console menu -option).

    -

    Controlling the layout of the Web Services Menu
    -The range of services that Jalview is able to access depends upon your -requirements, and local computational resources. However, when a large -number of resources are available, then the entries and sub menus in the -web services menu can quickly become unwieldly. The -options in the lower part of the dialog box enable you to control the -display of each type of analysis service client in the web services -menu. In addition, indexing options are provided that enable you to -define the layout of the menus provided for JABAWS services by sorting -them into submenus according to analysis type and/or host server.

    -

    The web services preferences panel was added in Jalview -2.6, and server status indications added in Jalview 2.8.

    -

    Web Services Invalid -URL warnings
    -Jalview may inform you of any problems contacting the web services by -showing a dialog box like the one below:
    -

    Web Services Invalid URL Warning dialog box
    -Web Services Invalid URL Warning dialog box
    -
    -Note: this warning will be shown if you are running the Jalview desktop -without any network connection, or if you have configured -JABA services -which cannot be accessed from your location. Should you wish to disable -these warnings, then uncheck the -Display warnings -check box in the web services preferences. -

    -

    The web services warnings dialog box was added in -Jalview 2.6.1

    +

    + Jalview includes a range of web services clients for data retrieval + and analysis. The Web Services menu found in each alignment + window provides access to some of these services, and is configured + via the web services preference dialog box, available from + the Preferences panel from the Tools→Preferences... + menu from the Jalview Desktop window's menu bar. +

    +

    +

    + Web Services Preferences Panel
    Web Services Preference Panel +
    +

    +

    + Configuring the list of JABAWS servers
    The + main area of the panel shows the list of JABAWS + servers that Jalview is currently aware of. The list includes a + colour coded status: green indicates that all services are available + for a given server, amber signifies that one or more services on the + server are not fully functional, and red highlights servers that + could not be contacted or are not functional for some other reason. +

    +

    + A server's URL may be added, edited by double clicking on it, or + deleted by selecting it and using the buttons below. After adding or + editing a server's URL, you will be asked if you wish to test the + server. If you wish to do so, then first ensure you can view the new + server's test report, which will be output on Jalview's standard + console output (you can open Jalview's built in console viewer via + the Tools→Java Console menu option). +

    +

    + Controlling the layout of the Web Services Menu
    + The range of services that Jalview is able to access depends upon + your requirements, and local computational resources. However, when + a large number of resources are available, then the entries and sub + menus in the web services menu can quickly become + unwieldly. The options in the lower part of the dialog box enable + you to control the display of each type of analysis service client + in the web services menu. In addition, indexing options are provided + that enable you to define the layout of the menus provided for + JABAWS services by sorting them into submenus according to analysis + type and/or host server. +

    +

    + The web services preferences panel was added in Jalview + 2.6, and server status indications added in Jalview 2.8. +

    +

    + Web Services Invalid URL + warnings
    Jalview may inform you of any problems + contacting the web services by showing a dialog box like the one + below:
    +

    + Web Services Invalid URL Warning dialog box
    Web Services Invalid URL Warning dialog box +
    +
    + Note: this warning will be shown if you are + running the Jalview desktop without any network connection, or if you + have configured + JABA services which cannot be accessed from + your location. Should you wish to disable these warnings, then uncheck + the + Display warnings check box in the web services preferences. +

    +

    + The web services warnings dialog box was added in Jalview + 2.6.1 +

    -- 1.7.10.2