Annotation Panel Menus

From ac5cc638b08386985f91503c81b27263230046e3 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 17 Aug 2005 15:40:56 +0000 Subject: [PATCH] Web Services moved from Calculate --- help/help.jhm | 3 +- help/helpTOC.xml | 1 + help/html/menus/alignmentMenu.html | 670 ++++++++++++++++------------------- help/html/menus/alwannotations.html | 116 +++--- help/html/menus/alwcalculate.html | 130 +++---- help/html/menus/alwedit.html | 187 +++++----- help/html/menus/popupMenu.html | 10 +- help/html/menus/wsmenu.html | 46 +++ help/html/webServices/clustal.html | 2 +- help/html/webServices/clustalw.html | 17 +- help/html/webServices/index.html | 6 +- help/html/webServices/jnet.html | 170 ++++----- help/html/webServices/muscle.html | 8 +- 13 files changed, 648 insertions(+), 718 deletions(-) create mode 100755 help/html/menus/wsmenu.html diff --git a/help/help.jhm b/help/help.jhm index 5324b0b..7d884b3 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -50,7 +50,8 @@ - + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index c1a6812..0f476a5 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -47,6 +47,7 @@ + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index c935bd2..44ba59a3 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -4,367 +4,317 @@

Alignment Window Menus

File

Save As
- Save the alignment to local file. A file selection window will - open, use the "Files of type:" selection box to determine which - alignment format to save as.
-
Export
- Creates an alignment graphic with the current annotation, - alignment background colours and group colours. If the alignment is wrapped, the output will also - be wrapped and will have the same visible residue width as the - open alignment. - -
- HTML
  - Create a web page - from your alignment.
- EPS
  - Create an Encapsulated - Postscript file from your alignment.
- PNG
  - Create a Portable Network - Graphics file from your alignment.
  -
-
Output to Textbox
- The alignment will be displayed in plain text in a new window - which you can "Copy and Paste" using the pull down menu, or your - standard operating system copy and paste keys.
- Select the format of the text by selecting one of the following menu items. -
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
-
Print
- Jalview will print the alignment using the current fonts and - colours of your alignment. If the alignment has annotations visible, these - will be printed below the alignment. If the alignment is wrapped the number - of residues per line of your alignment will depend on the paper width or - your alignment window width, whichever is the smaller.
-
Load Associated Tree
- Jalview can view trees stored in - the Newick file format, and associate them with the - alignment. Note: the ids of the tree file and your alignment - MUST be the same.
-
Close
- Close the alignment window. Make sure you have - saved your alignment before you close - either as a Jalview - project or by using the Save As menu.
-

Edit

-
-
Undo
- This will undo any edits you make to the alignment. This applies to insertion - or deletion of gaps, cutting residues or sequences from the alignment or - pasting sequences to the current alignment or sorting the - alignment. NOTE: It DOES NOT undo colour - changes, adjustments to group sizes, or changes to the annotation panel.
-
-
Redo
- Any actions which you undo can be redone using redo.
-
-
Cut
- This will make a copy of the currently selected residues before - removing them from your alignment. Click on a sequence name if you wish - to select a whole sequence.
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
-
-
Copy
- Copies the currently selected residues to the system - clipboard - you can also do this by pressing <CTRL> and C - (<APPLE> and C on MacOSX).
- If you try to paste the clipboard contents to a text editor, you will see - the format of the copied residues is a tab separated list:
-
-NAME START_RES END_RES SEQUENCE -

-
-
Paste -
-
To New Alignment
- A new alignment window will be created from sequences previously - copied or cut to the system clipboard.
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
-
Add To This Alignment
- Copied sequences from another alignment window can be added - to the current Jalview alignment.
-
-
-
-
Delete
- This will delete the currently selected residues - without copying them to the clipboard. Like the other edit - operations, this can be undone with Undo.
-
-
Select All
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
-
Deselect All
- Removes the current selection box (red dashed box) from the - alignment window. All selected sequences, residues and marked columns will - be deselected.
- Use <ESCAPE> to deselect all.
-
-
Invert Selection
- Any sequence ids currently not selected will replace the current - selection.
-
-
Undefine Groups
- The alignment will be reset with no defined groups.
WARNING: - This cannot be undone.
-
-
Remove Left
- If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
-
-
Remove Right
- If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
-
-
Remove Empty Columns
- All columns which only contain gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences. -
-
-
Remove All Gaps
- All gap characters ("-", ".") will be deleted from - the alignment.
- You may set the default gap character in preferences. -
-
-
Remove Redundancy
- Selecting this option brings up a window asking you to select - a threshold. If the percentage identity between any two sequences - (under the current alignment) exceeds this - value then one of the sequences (the shorter) is discarded. Press the "Apply" - button to remove redundant sequences. The "Undo" button will undo the last - redundancy deletion.
-
-
Pad Gaps
- Adds gaps to the end of all the sequences so they - are all the same length. This is useful for making a tree using - unaligned sequences.
- You may set the default gap character in preferences. -
-
-

Search

-
-
Find
- Select this to search - for residues, sequence name or residue position within the alignment.
-
-

View

-
-
Font
- Change the font of the display from the - "Choose Font" dialog box, which is shown when this - item is selected.
-
-
Wrap
- When ticked, the alignment display is - "wrapped" to the - width of the alignment window. This is useful if your alignment - has only a few sequences to view its full width at once.
- Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each - sequence row.
- NOTE: When in wrapped alignment view, the - alignment cannot be edited or have regions selected on it.
-
-
Show Full Sequence ID
- If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format NAME/START-END
-
-
Boxes
- If this is selected the background of a residue will be coloured using the - selected background colour. Useful if used in conjunction with "Colour - Text."
-
-
Text
- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
-
-
Colour Text
- If this is selected the residues will be coloured according - to the background colour associated with that residue. The colour is slightly - darker than background so the amino acid symbol remains visible.
-
-
Show Gaps
- When this is selected, gap characters will be displayed as "." - or "-". If unselected, then gap characters will appear as blank spaces. -
- You may set the default gap character in preferences.
-
-
Show Annotations
- If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the conservation - calculation, quality calculation and consensus values as bar charts.
-
-
Sequence Features
- If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features from the EBI. Features which are - 1 residue in length are coloured red, sequences longer than 1 residue are - coloured blue. Move the mouse over a coloured feature to display the details - of the feature.
- Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
-
-
Overview Window
- A scaled version of the alignment will be displayed in a small - window. A red box will indicate the currently visible area of the alignment. - Move the visible region using the mouse.
-
-

Colour

-
-
Apply Colour To All Groups
- If this is selected, any changes made to the background colour - will be applied to all currently defined groups.
-
-
Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, - Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried - Index, Nucleotide, User Defined
- See colours for - a description of all colour schemes.
-
-
By Conservation
- See Colouring - by Conservation.
-
-
Modify Conservation Threshold
- Use this to display the conservation threshold slider window. - Useful if the window has been closed, or if the 'by - conservation' option appears to be doing nothing!
-
Above Identity Threshold
- See Above Percentage - Identity.
-
-
Modify Identity Threshold
- Use this to set the threshold value for colouring above Identity. - Useful if the window has been closed.
-
-

Calculate

-
-
Sort -
-
by ID
- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-
-
by Group
- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-
-
by Pairwise Identity
- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
-
-
- The Sort menu will - have some additional options if you have just done a multiple - alignment calculation, or opened a tree viewer window.
-
-
Calculate Tree -
Functions for calculating trees on the alignment or the - currently selected region. See calculating trees. -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
-
-
-
Pairwise Alignments
- Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
-
-
Principal Component Analysis
- Shows a spatial clustering of the sequences based on the - BLOSUM62 scores in the alignment. See Principal Component Analysis. -
-
-
Web Service
- - Selecting one of the following menu items starts a remote service - on compute facilities at the University of Dundee. You need a - continuous network connection in order to use these services - through Jalview. - -
-
Clustal Alignment
- Submits all, or just the currently selected sequences for alignment with clustal W.
-
Clustal Realign
- Submits the alignment or currently selected region for - re-alignment with clustal W. Use this if you have added some - new sequences to an existing alignment.
-
Muscle Alignment
- Submits all, or jut the currently selected sequences for - alignment using Muscle. Do not use this if you are working with - nucleic acid sequences.
-
JNet
- Secondary structure prediction by network consensus. The - behaviour of this calculation depends on the current selection: +
File +
+
Save As
+ Save the alignment to local file. A file selection window + will open, use the "Files of type:" selection box to determine + which alignment format to save as.
+
Export
+ Creates an alignment graphic with the current annotation, alignment background + colours and group colours. If the alignment is wrapped, the output will also be wrapped + and will have the same visible residue width as the open alignment. +
+
HTML
+ Create a web page + from your alignment.
+
EPS
+ Create an Encapsulated + Postscript file from your alignment.
+
PNG
+ Create a Portable Network + Graphics file from your alignment.
+
+
+
Output to Textbox
+ The alignment will be displayed in plain text in a new window + which you can "Copy and Paste" using the pull down menu, or + your standard operating system copy and paste keys.
+ Select the format of the text by selecting one of the following menu items. +
+
FASTA
+
MSF
+
CLUSTAL
+
BLC
+
PIR
+
PFAM
+
+
+
Print
+ Jalview will print the alignment using the current fonts + and colours of your alignment. If the alignment has annotations visible, + these will be printed below the alignment. If the alignment is wrapped + the number of residues per line of your alignment will depend on the paper + width or your alignment window width, whichever is the smaller.
+
Load Associated Tree
+ Jalview can view trees stored in the Newick + file format, and associate them with the alignment. Note: the ids of the + tree file and your alignment MUST be the same.
+
Close
+ Close the alignment window. Make sure you have saved your + alignment before you close - either as a Jalview project or by using the + Save As menu.
+
+
+
+
Edit +
+
Undo
+ This will undo any edits you make to the alignment. This applies to insertion + or deletion of gaps, cutting residues or sequences from the alignment + or pasting sequences to the current alignment or sorting the alignment. + NOTE: It DOES NOT undo colour changes, adjustments to + group sizes, or changes to the annotation panel.
+
Redo
+ Any actions which you undo can be redone using redo.
+
Cut
+ This will make a copy of the currently selected residues + before removing them from your alignment. Click on a sequence name if + you wish to select a whole sequence.
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
+
Copy
+ Copies the currently selected residues to the system clipboard - you + can also do this by pressing <CTRL> and C (<APPLE> and C on + MacOSX).
+ If you try to paste the clipboard contents to a text editor, you will + see the format of the copied residues is a tab separated list
+ NAME START_RES END_RES SEQUENCE
+
Paste +
+
To New Alignment
+ A new alignment window will be created from sequences + previously copied or cut to the system clipboard.
+ Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
+
Add To This Alignment
+ Copied sequences from another alignment window can be + added to the current Jalview alignment.
+
+
+
Delete
+ This will delete the currently selected residues without + copying them to the clipboard. Like the other edit operations, this can + be undone with Undo.
+
Select All
+ Selects all the sequences and residues in the alignment. +
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
+
Deselect All
+ Removes the current selection box (red dashed box) from the + alignment window. All selected sequences, residues and marked columns + will be deselected.
+ Use <ESCAPE> to deselect all.
+
Invert Selection
+ Any sequence ids currently not selected will replace the + current selection.
+
Undefine Groups
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
Remove Left
+ If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, mouse + click the scale bar above the alignment. Click again to unmark a column, + or select "Deselect All" to deselect all columns.
+
Remove Right
+ If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, mouse + click the scale bar above the alignment. Click again to unmark a column, + or select "Deselect All" to deselect all columns.
+
Remove Empty Columns
+ All columns which only contain gap characters ("-", + ".") will be deleted.
+ You may set the default gap character in preferences. +
+
Remove All Gaps
+ Gap characters ("-", ".") will be deleted from + the selected area of the alignment. If no selection is made, ALL the gaps + in the alignment will be removed.
+ You may set the default gap character in preferences. +
+
Remove Redundancy
+ Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between any two sequences (under + the current alignment) exceeds this value then one of the sequences (the + shorter) is discarded. Press the "Apply" button to remove redundant + sequences. The "Undo" button will undo the last redundancy deletion.
+
Pad Gaps
+ Adds gaps to the end of all the sequences so they are all + the same length. This is useful for making a tree using unaligned sequences.
+ You may set the default gap character in preferences. +
+
+
+
+
Search +
+
Find
+ Select this to search + for residues, sequence name or residue position within the alignment. +
+
+
+
+
View +
+
Font
+ Change the font of the display from the "Choose Font" + dialog box, which is shown when this item is selected.
+
Wrap
+ When ticked, the alignment display is "wrapped" + to the width of the alignment window. This is useful if your alignment + has only a few sequences to view its full width at once.
+ Options are available to show the residue numbering at the start and/or + end of an alignment as well as showing the alignment position above each + sequence row.
+ NOTE: When in wrapped alignment view, the alignment cannot + be edited or have regions selected on it.
+
Show Full Sequence ID
+ If this box is selected the sequence name will have the start + and end position of the sequence appended to the name, in the format NAME/START-END
+
Boxes
+ If this is selected the background of a residue will be coloured using + the selected background colour. Useful if used in conjunction with "Colour + Text."
+
Text
+ If this is selected the residues will be displayed using + the standard 1 character amino acid alphabet.
+
Colour Text
+ If this is selected the residues will be coloured according + to the background colour associated with that residue. The colour is slightly + darker than background so the amino acid symbol remains visible.
+
Show Gaps
+ When this is selected, gap characters will be displayed as + "." or "-". If unselected, then gap characters will + appear as blank spaces.
+ You may set the default gap character in preferences.
+
Show Annotations
+ If this is selected the "Annotation Panel" will + be displayed below the alignment. The default setting is to display the + conservation calculation, quality calculation and consensus values as + bar charts.
+
Sequence Features
+ If the sequence names are Swissprot entries Jalview will + use the names to retrieve sequence + features from the EBI. Features which are 1 residue in length are + coloured red, sequences longer than 1 residue are coloured blue. Move + the mouse over a coloured feature to display the details of the feature. +
+ Note: The retrieved information will update the sequence start and end + labels if they are incorrect.
+
Overview Window
+ A scaled version of the alignment will be displayed in a + small window. A red box will indicate the currently visible area of the + alignment. Move the visible region using the mouse.
+
+
+
Colour +
+
Apply Colour To All Groups
+ If this is selected, any changes made to the background colour + will be applied to all currently defined groups.
+
Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage + Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, + Turn Propensity, Buried Index, Nucleotide, User Defined
+ See colours for + a description of all colour schemes.
+
By Conservation
+ See Colouring + by Conservation.
+
Modify Conservation Threshold
+ Use this to display the conservation threshold slider window. + Useful if the window has been closed, or if the 'by conservation' option + appears to be doing nothing!
+
Above Identity Threshold
+ See Above Percentage + Identity.
+
Modify Identity Threshold
+ Use this to set the threshold value for colouring above Identity. + Useful if the window has been closed.
+
+
+
+
Calculate +
+
Sort +
+
by ID
+ This will sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be inverted.
+
by Group
+ This will sort the sequences according to sequence name. + If the sort is repeated, the order of the sorted sequences will be + inverted.
+
by Pairwise Identity
+ This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put + at the top.
+
The Sort menu will + have some additional options if you have just done a multiple alignment + calculation, or opened a tree viewer window.
+
+
+
Calculate Tree
+ Functions for calculating trees on the alignment or the currently + selected region. See calculating trees. +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
Pairwise Alignments
+ Applies Smith and Waterman algorithm to selected sequences. See pairwise + alignments.
+
Principal Component Analysis
+ Shows a spatial clustering of the sequences based on the BLOSUM62 + scores in the alignment. See Principal + Component Analysis.
+
+
+
+
Web Service
+ Selecting one of the following menu items starts a remote service + on compute facilities at the University of Dundee. You need a continuous network + connection in order to use these services through Jalview. +
+
Alignment +
+
ClustalW Multiple Sequence Alignment
+ Submits all, or just the currently selected sequences for alignment + with clustal W.
+
ClustalW Multiple Sequence Alignment Realign
+ Submits the alignment or currently selected region for re-alignment + with clustal W. Use this if you have added some new sequences to an + existing alignment.
+
Muscle Multiple Protein Sequence Alignment
+ Submits all, or jut the currently selected sequences for alignment + using Muscle. Do not use this if you are working with nucleic acid + sequences.
+
+
+
Secondary Structure Prediction
-
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 -that was first clicked on). -
- +
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. The behaviour + of this calculation depends on the current selection:
+
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 that was first clicked + on).
+
+
+
+

-
-
-

-

diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html index f7b62ca..5655a5a 100755 --- a/help/html/menus/alwannotations.html +++ b/help/html/menus/alwannotations.html @@ -1,58 +1,58 @@ - - -Annotation Panel Menus - - -
Annotation Panel Menus
-
-
-Annotation Label Popup Menu
-This menu is opened by clicking anywhere on the annotation row labels -area (below the sequence ID area). -
-
-Add New Row
-Adds a new, named annotation row (a dialog box will pop up for you -to enter the label for the new row). -
Hide Row
-Hides the annotation row whose label was clicked in order to bring -up the menu. -
Delete Row
-Deletes the annotation row whose label was clicked in order to bring -up the menu. -
Show All Hidden Rows
-Shows all hidden annotation rows. -
Show Values in Text Box
-Opens a text box with a list of comma-separated values -corresponding to the annotation (numerical or otherwise) at each -position in the row. This is useful to export alignment quality -measurements for further analysis. -
-
-
-
Annotation Popup Menu
This menu is opened when -right-clicking on the selected positions of an annotation. -
-
Helix
Mark selected positions with a helix glyph (a red -oval), and optional text label (see below). Consecutive ovals -will be rendered as an unbroken red line. -
-
Sheet
Mark selected positions with a sheet glyph (a green -arrow oriented from left to right), and optional text label (see -below). Consecutive arrows will be joined together to form a single -green arrow. -
-
Label
Sets the text label at the selected positions. If -more that one consecutive position is marked with the same label, only -the first position's label will be rendered. -
-
Colour
Changes the colour of the annotation text label. -
-
Remove Annotation
Blanks any annotation at the selected positions on -the row. Note: This cannot be undone -
-
-
-
- - + + +Annotation Panel Menus + + +
Annotation Panel Menus
+
+
Annotation Label Popup Menu
+ This menu is opened by clicking anywhere on the annotation row labels + area (below the sequence ID area). +
+
Add New Row
+ Adds a new, named annotation row (a dialog box will pop up for you + to enter the label for the new row).
+
Hide Row
+ Hides the annotation row whose label was clicked in order to bring + up the menu.
+
Delete Row
+ Deletes the annotation row whose label was clicked in order to bring + up the menu.
+
Show All Hidden Rows
+ Shows all hidden annotation rows.
+
Show Values in Text Box
+ Opens a text box with a list of comma-separated values corresponding + to the annotation (numerical or otherwise) at each position in the row. + This is useful to export alignment quality measurements for further analysis. +
+
Ignore Gaps in Consensus
+ If this checkbox is selected, all conensus calculations performed in the + current Alignment window will not include gaps in the consensus calculation.
+
+
+
Annotation Popup Menu
+ This menu is opened when right-clicking on the selected positions + of an annotation. +
+
Helix
+ Mark selected positions with a helix glyph (a red oval), and optional + text label (see below). Consecutive ovals will be rendered as an unbroken + red line.
+
Sheet
+ Mark selected positions with a sheet glyph (a green arrow oriented + from left to right), and optional text label (see below). Consecutive + arrows will be joined together to form a single green arrow.
+
Label
+ Sets the text label at the selected positions. If more that one consecutive + position is marked with the same label, only the first position's label + will be rendered.
+
Colour
+ Changes the colour of the annotation text label.
+
Remove Annotation
+ Blanks any annotation at the selected positions on the row. Note: + This cannot be undone
+
+
+
+ + diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 4d4264b..97bff22 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -3,94 +3,48 @@
Alignment Window Calculate Menu
+Calculate
-
Calculate
+
Sort +
+
by ID
+ This will sort the sequences according to sequence name. If the sort is + repeated, the order of the sorted sequences will be inverted.
+
by Group
+ This will sort the sequences according to sequence name. + If the sort is repeated, the order of the sorted sequences will be inverted. +
+
by Pairwise Identity
+ This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put at + the top.
+
The Sort menu will have + some additional options if you have just done a multiple alignment calculation, + or opened a tree viewer window.
+
+
+
+
Calculate Tree
+ Functions for calculating trees on the alignment or the currently selected + region. See calculating trees. +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
+
Pairwise Alignments
+ Applies Smith and Waterman algorithm to selected sequences. See pairwise + alignments.
+
+
Principal Component Analysis
+ Shows a spatial clustering of the sequences based on the BLOSUM62 scores + in the alignment. See Principal Component + Analysis.
+

-
-
-
Sort -
-
by ID
- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-
-
by Group
- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-
-
by Pairwise Identity
- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
-
-
- The Sort menu will - have some additional options if you have just done a multiple - alignment calculation, or opened a tree viewer window.
-
-
Calculate Tree -
Functions for calculating trees on the alignment or the - currently selected region. See calculating trees. -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
-
-
-
Pairwise Alignments
- Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
-
-
Principal Component Analysis
- Shows a spatial clustering of the sequences based on the - BLOSUM62 scores in the alignment. See Principal Component Analysis. -
-
-
Web Service
- - Selecting one of the following menu items starts a remote service - on compute facilities at the University of Dundee. You need a - continuous network connection in order to use these services - through Jalview. - -
-
Clustal Alignment
- Submits all, or just the currently selected sequences for alignment with clustal W.
-
Clustal Realign
- Submits the alignment or currently selected region for - re-alignment with clustal W. Use this if you have added some - new sequences to an existing alignment.
-
Muscle Alignment
- Submits all, or jut the currently selected sequences for - alignment using Muscle. Do not use this if you are working with - nucleic acid sequences.
-
JNet
- Secondary structure prediction by network consensus. The - behaviour of this calculation depends on the current selection: -
-
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 - that was first clicked on). -
-
-
-

-
-
- - + diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index dcd7d68..4e0c8b0 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -3,111 +3,90 @@
Alignment Window Edit Menu
+Edit
-
Edit
+
Undo
+ This will undo any edits you make to the alignment. This applies to insertion + or deletion of gaps, cutting residues or sequences from the alignment or pasting + sequences to the current alignment or sorting the alignment. NOTE: + It DOES NOT undo colour changes, adjustments to group sizes, or changes to + the annotation panel.
+
Redo
+ Any actions which you undo can be redone using redo.
+
Cut
+ This will make a copy of the currently selected residues before + removing them from your alignment. Click on a sequence name if you wish to + select a whole sequence.
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
+
Copy
+ Copies the currently selected residues to the system clipboard - you can + also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX). +
+ If you try to paste the clipboard contents to a text editor, you will see + the format of the copied residues is a tab separated list
+ NAME START_RES END_RES SEQUENCE
+
Paste +
+
To New Alignment
+ A new alignment window will be created from sequences previously + copied or cut to the system clipboard.
+ Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
+
Add To This Alignment
+ Copied sequences from another alignment window can be added + to the current Jalview alignment.
+
+
+
Delete
+ This will delete the currently selected residues without copying + them to the clipboard. Like the other edit operations, this can be undone + with Undo.
+
Select All
+ Selects all the sequences and residues in the alignment.
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
+
Deselect All
+ Removes the current selection box (red dashed box) from the alignment + window. All selected sequences, residues and marked columns will be deselected. +
+ Use <ESCAPE> to deselect all.
+
Invert Selection
+ Any sequence ids currently not selected will replace the current + selection.
+
Undefine Groups
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
Remove Left
+ If the alignment has marked columns, the alignment will be trimmed + to the left of the leftmost marked column. To mark a column, mouse click the + scale bar above the alignment. Click again to unmark a column, or select "Deselect + All" to deselect all columns.
+
Remove Right
+ If the alignment has marked columns, the alignment will be trimmed + to the left of the leftmost marked column. To mark a column, mouse click the + scale bar above the alignment. Click again to unmark a column, or select "Deselect + All" to deselect all columns.
+
Remove Empty Columns
+ All columns which only contain gap characters ("-", + ".") will be deleted.
+ You may set the default gap character in preferences. +
+
Remove All Gaps
+ Gap characters ("-", ".") will be deleted from the + selected area of the alignment. If no selection is made, ALL the gaps in the + alignment will be removed.
+ You may set the default gap character in preferences. +
+
Remove Redundancy
+ Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between any two sequences (under the + current alignment) exceeds this value then one of the sequences (the shorter) + is discarded. Press the "Apply" button to remove redundant sequences. + The "Undo" button will undo the last redundancy deletion.
+
Pad Gaps
+ Adds gaps to the end of all the sequences so they are all the + same length. This is useful for making a tree using unaligned sequences.
+ You may set the default gap character in preferences. +

-
-
-
Undo
- This will undo any edits you make to the alignment. This applies to insertion - or deletion of gaps, cutting residues or sequences from the alignment or - pasting sequences to the current alignment or sorting the - alignment. NOTE: It DOES NOT undo colour - changes, adjustments to group sizes, or changes to the annotation panel.
-
-
Redo
- Any actions which you undo can be redone using redo.
-
-
Cut
- This will make a copy of the currently selected residues before - removing them from your alignment. Click on a sequence name if you wish - to select a whole sequence.
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
-
-
Copy
- Copies the currently selected residues to the system - clipboard - you can also do this by pressing <CTRL> and C - (<APPLE> and C on MacOSX).
- If you try to paste the clipboard contents to a text editor, you will see - the format of the copied residues is a tab separated list:
-
-NAME START_RES END_RES SEQUENCE -

-
-
Paste -
-
To New Alignment
- A new alignment window will be created from sequences previously - copied or cut to the system clipboard.
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
-
Add To This Alignment
- Copied sequences from another alignment window can be added - to the current Jalview alignment.
-
-
-
-
Delete
- This will delete the currently selected residues - without copying them to the clipboard. Like the other edit - operations, this can be undone with Undo.
-
-
Select All
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
-
Deselect All
- Removes the current selection box (red dashed box) from the - alignment window. All selected sequences, residues and marked columns will - be deselected.
- Use <ESCAPE> to deselect all.
-
-
Invert Selection
- Any sequence ids currently not selected will replace the current - selection.
-
-
Undefine Groups
- The alignment will be reset with no defined groups.
WARNING: - This cannot be undone.
-
-
Remove Left
- If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
-
-
Remove Right
- If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
-
-
Remove Empty Columns
- All columns which only contain gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences. -
-
-
Remove All Gaps
- All gap characters ("-", ".") will be deleted from - the alignment.
- You may set the default gap character in preferences. -
-
-
Remove Redundancy
- Selecting this option brings up a window asking you to select - a threshold. If the percentage identity between any two sequences - (under the current alignment) exceeds this - value then one of the sequences (the shorter) is discarded. Press the "Apply" - button to remove redundant sequences. The "Undo" button will undo the last - redundancy deletion.
-
-
Pad Gaps
- Adds gaps to the end of all the sequences so they - are all the same length. This is useful for making a tree using - unaligned sequences.
- You may set the default gap character in preferences. -
-
-
+

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 14dc178..94ffb3c 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -52,11 +52,15 @@ -> Sequence Features" before associating a PDB file with a sequence.
If the sequence has a PDB file associated with it Jalview will display - a 3D interactive viewer of the file.
-
- + a 3D interactive viewer of the file. +

Link
+ This menu item lists all links which have been set up in the Preferences + Connections tab. It is only displayed when you right click (Apple click) on + a sequence id.
+
+

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html new file mode 100755 index 0000000..e2a9a4d --- /dev/null +++ b/help/html/menus/wsmenu.html @@ -0,0 +1,46 @@ + +Web Service Menu + + +

Web Service Menu

+ Selecting one of the following menu items starts a remote service + on compute facilities at the University of Dundee. You need a continuous network + connection in order to use these services through Jalview.

Alignment +
- ClustalW Multiple Sequence Alignment
  + Submits all, or just the currently selected sequences for alignment + with clustal W.
- ClustalW Multiple Sequence Alignment Realign
  + Submits the alignment or currently selected region for re-alignment + with clustal W. Use this if you have added some new sequences to an existing + alignment.
- Muscle Multiple Protein Sequence Alignment
  + Submits all, or jut the currently selected sequences for alignment + using Muscle. Do not use this if you are working with nucleic acid sequences.
+
Secondary Structure Prediction +
- JPred Secondary Structure Prediction
  + Secondary structure prediction by network consensus. The behaviour + of this calculation depends on the current selection:
- 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 that was first clicked + on).
+

+ + diff --git a/help/html/webServices/clustal.html b/help/html/webServices/clustal.html index 94f0bee..918ec3b 100755 --- a/help/html/webServices/clustal.html +++ b/help/html/webServices/clustal.html @@ -1,7 +1,7 @@ Clustal Alignment -

Calculations→Web Service→Clustal Alignment..

Web Service→Alignment→ClustalW Multiple Sequence Alignment

When this option is selected a progress window will appear giving you a message about whether your process is running. The alignment is sent to the Barton Group cluster and remotely aligned using Clustalw program.

diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html index 3258494..96b45b7 100755 --- a/help/html/webServices/clustalw.html +++ b/help/html/webServices/clustalw.html @@ -16,16 +16,13 @@ penalties and weight matrix choice.

There are two versions of this alignment function, which will operate on the selected region, if any, or the whole sequence set:

Calculations→Web Service→Clustal -Alignment..
-Aligns using the clustalW program, ignoring any gaps in the submitted -sequence set. -
Calculations→Web Service→Clustal -Realign..
-Submits the sequences with existing gaps to clustalW, which will -preserve existing gaps and re-align those regions which are not optimal. -
Web Service→Alignment→ClustalW Multiple Sequence Alignment
+ Aligns using the clustalW program, ignoring any gaps in the submitted sequence + set.
Web Service→Alignment→ClustalW Mulitple Sequence Alignment + Realign
+ Submits the sequences with existing gaps to clustalW, which will preserve + existing gaps and re-align those regions which are not optimal.

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index de04ec1..d90fa85 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -2,9 +2,9 @@ Web Services

Web services

A variety of web services are available from the Alignment window's - Calculations→Web Service menu. -

+ +

A variety of web services are available from the Alignment window's + Web Service menu.

Jalview's distributed computations are SOAP based services exposing protein sequence alignment and secondary structure prediction programs. These services actually run on the cluster based in the School of Life Sciences, University of diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 93c13d8..52d8740 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -1,85 +1,85 @@ - - -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 structure. The JNet -method uses several different prediction methods and decides on the -most likely prediction via a jury network.
-

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 Calculations→Web -Service→JNet... 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 -that was first clicked on). -

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 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 structure. The JNet +method uses several different prediction methods and decides on the +most likely prediction via a jury network.
+

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→Muscle Alignment 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 +that was first clicked on). +

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.

+ + diff --git a/help/html/webServices/muscle.html b/help/html/webServices/muscle.html index 58b29bc..1ce576a 100755 --- a/help/html/webServices/muscle.html +++ b/help/html/webServices/muscle.html @@ -7,10 +7,8 @@ Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Research 32(5), 1792-97.

-This alignment method is applied to the selected region, if any, or -the whole sequence set when the Calculations→Web -Service→Muscle Alignment... menu is selected. -

This alignment method is applied to the selected region, if any, or the whole + sequence set when the Web Service→Secondary Structure Prediction→Muscle + Alignment menu is selected.

-- 1.7.10.2