Input/Ouput

Principal components analysis is a technique for examining the -structure of complex datasets. The components are a set of dimensions -formed from the measured values in the dataset, and the principle +structure of complex data sets. The components are a set of dimensions +formed from the measured values in the data set, and the principle 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 principle axis, and the other axes correspond to less extreme -patterns of variation in the dataset. +patterns of variation in the data set.

In this case, the components are generated by an eigenvector @@ -29,21 +29,21 @@ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt= href="http://industry.ebi.ac.uk/SeqSpace/">http://industry.ebi.ac.uk/SeqSpace) at the EBI.

This is an interactive display of the sequences positioned within the similarity space. The colour of each sequence point is the same - as the sequence group coloring, white if no colour has been + 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.

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 alignment window. Rectanglar region - based selection is also possible, by holding the 's' key whilst + corresponding sequence in the alignment window. Rectangular region + based selection is also possible, by holding the 'S' key whilst left-clicking and dragging the mouse over the display.

Initially, the display shows the first three components of the diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index e97e3b0..1f3d464 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -3,13 +3,9 @@

Selecting this option brings up a window asking you to select a threshold. - If the percentage identity between two sequences (based on the - current alignment) exceeds this value one of the + If the percentage identity between two sequences exceeds this value one of the sequences (the shorter) is discarded. The redundancy calculation is done when - the Apply button is pressed, and the undo button recovers the - original set or any previously calculated subset. The detection of - redundant sequences involves a pairwise comparison of all the - sequences, so you may have to wait a few moments when applying this to - large sequence sets.

If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse -order for that property. In the case of trees and alignment orderings, Jalview will +

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.

Selecting sequence ids at the leaves of the tree selects the @@ -23,14 +23,14 @@

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 occured. Groups + of the tree spanning the depth where the mouse-click occurred. Groups are created containing sequences at the leaves of each connected - subtree. These groups are each given a different colour, which are + 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 @@ -47,7 +47,7 @@ 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, or additional leaves from sequences not present in the associated -alignment. +alignment.

The view menu contains options controlling the way a tree is rendered and labelled:

Gaps are coloured white. If a residue matchs the consensus sequence residue - at that position it is colored dark blue. If it does not match the consensus - residue but the 2 residues have a positive Blosum62 score, it is colored light +

Gaps are coloured white. If a residue matches the consensus sequence residue + at that position it is coloured dark blue. If it does not match the consensus + residue but the 2 residues have a positive Blosum62 score, it is coloured light blue.

Zappo Colours

- The residues are coloured according to their physico-chemical properties as + The residues are coloured according to their physicochemical properties as follows:

diff --git a/help/html/io/index.html b/help/html/io/index.html index b067512..bd2a790 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,13 +1,13 @@ -Input/Ouput +Input/Output

Input

Jalview can read alignment files in any of the following standard formats:

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

The EBI has examples of +

The EBI has examples of these file formats.

Additionally annotated alignments can be read in from the Jalview format.

Use the "Input Alignment" menu at the top of the main application +

Use the "Input Alignment" menu at the top of the main application window to read in files from

the local file system

Output

Each alignment, whether it is the original or an edited version may be saved +

Each alignment, whether it is the original or an edited version may be saved in the standard formats

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

You may save annotated alignments in the Jalview file format.

Export

The alignment may also be saved as a HTML web page.

You may save a Portable Networks Graphics (PNG) image of your alignment.

You may save the alignment as an Encapsulated Postscript file. This is a vector - graphics file which may be modified in various graphics applications, such as +

You may save the alignment as an Encapsulated Postscript file. This is a vector + graphics file which may be modified in various graphics applications, such as Adobe Illustrator.

- Tip: When importing to a Microsoft document, a snapshot image is taken of your - file - this will be blurred. Right-click the image and choose "Edit image." + Tip: When importing to a Microsoft document, a snapshot image is taken of your + file - this will be blurred. Right-click the image and choose "Edit image." This will restore the high quality EPS file format output.
- NB. Mac OSX users will find that eps files are automatically converted into + NB. Mac OSX users will find that eps files are automatically converted into PDF files.

The alignment can be printed from a local printer.

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 + 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 output maintaining the 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. - + Creates an alignment output maintaining the 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 + Create a web page 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 + 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. + Select the format of the text by selecting one of the following menu items.

FASTA

MSF
@@ -45,63 +45,63 @@

Print
- Jalview will print the alignment using the current fonts and - coloursof 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 + 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 load in trees which are in the Newick file format - and associate them with a particular alignment. Note: the ids of the tree + Jalview can load in trees which are in the Newick file format + and associate them with a particular alignment. Note: the ids of the tree file and your alignment MUST be the same.

Close
- Close the alignment window. Be aware that changes to your alignment - will not be save unless specifically actioned from the "Save As" + Close the alignment window. Be aware that changes to your alignment + will not be save unless specifically actioned from 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. It - DOES NOT undo colour changes or adjustments to group sizes affect the annotation + 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. It + DOES NOT undo colour changes or adjustments to group sizes affect 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 + 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. The - format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE + Copies the currently selected residues to the system clipboard. The + format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE
Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.

-
Paste +
Paste

To New Alignment
- A new alignment window will be created from sequences previously + 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 + Copied sequences from another alignment window can be added to the current Jalview alignment.

Delete
- This will delete the currently selected residues without making + This will delete the currently selected residues without making a copy of them first.

Select All
@@ -109,213 +109,213 @@ 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 + 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 + Any sequence ids currently not selected will replace the current selection.

Undefine Groups
- The alignment will be reset with no defined groups. WARNING: + 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, + 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, + 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 contain purely gap characters ("-", + All columns which contain purely gap characters ("-", ".") will be deleted.
- You may set the default gap character in preferences. + You may set the default gap character in preferences.

Remove All Gaps
- All gap characters ("-", ".") will be deleted from + All gap characters ("-", ".") will be deleted from the alignment.
- You may set the default gap character in preferences. + 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 two sequences exceeds this - value one of the sequences (the shorter) is discarded. Press the "Apply" - button to reomove redundant sequences.
+ Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between two sequences exceeds this + value one of the sequences (the shorter) is discarded. Press the "Apply" + button to remove redundant sequences.

Pad Gaps
- If the sequences in an alignment window are not all the same - length they can all be set to the length of the longest sequence by selecting - "Pad Gaps." Any sequences which are shorter than the longest sequence - in an alignment will have gap characters ("-" or ".") + If the sequences in an alignment window are not all the same + length they can all be set to the length of the longest sequence by selecting + "Pad Gaps." Any sequences which are shorter than the longest sequence + in an alignment will have gap characters ("-" or ".") appended to the beginning or end to make them equal length.
- You may set the default gap character in preferences. + You may set the default gap character in preferences.

Search

-
+

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

View

-
+

Font
- Change the font of the display. The default font can be set - from the "Choose Font" window, which is shown when the "Font + Change the font of the display. The default font can be set + from the "Choose Font" window, which is shown when the "Font Menu" is selected.

Wrap
- The default alignment display shows sequences in a single horizontal - row. If your alignment has only a few sequences you may wish to "Wrap" - the alignment so that the sequences are shown on multiple horizontal rows. - 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 + The default alignment display shows sequences in a single horizontal + row. If your alignment has only a few sequences you may wish to "Wrap" + the alignment so that the sequences are shown on multiple horizontal rows. + 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: In the current version the wrap alignment should be used for viewing, + NOTE: In the current version the wrap alignment should be used for viewing, not editing.

Show Full Sequence ID
- If this box is selected the sequence name will have the start + 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 + 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 + 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 + 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 to enable the residue to be read.

Show Gaps
- If this is selected gap characters will be displayed as "." - or "-". If unselected gap characters will appear as blank spaces. + If this is selected gap characters will be displayed as "." + or "-". If unselected 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 - calulation, quality calculation and consensus values as bar charts.
+ 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 + 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 + 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. + 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 + If this is selected, any changes made to the background colour will be applied to all currently defined groups.

-
None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, - Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried +
None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, User Defined
- See colours for + See colours for a description of all colour schemes.

By Conservation
- See Colouring + See Colouring by Conservation.

Modify Conservation Threshold
- Use this to display the conservation threshold slider window. + Use this to display the conservation threshold slider window. Useful if the window has been closed.

Above Identity Threshold
- See Above Percentage + See Above Percentage Identity.

Modify Identity Threshold
- Use this to set the threshold value for colouring above Identity. + Use this to set the threshold value for colouring above Identity. Useful if the window has been closed.

Calculate

-
+

-
Sort +
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. + 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. + 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 + This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put at the top.

-
Calculate Tree +
Calculate Tree

Average Distance Using % Identity

Neighbour Joining Using % Identity

Average Distance Using Blosum62

Neighbour Joining Using Blosum62
- See calculating trees. + See calculating trees.

-
Paiwise Alignments
+
Pairwise Alignments
See pairwise alignments.

Principal Component Analysis
- See Principal Component Analysis. + See Principal Component Analysis.

Web Service
- +
- Selecting one of the following menu items will start a remote service - on the high powered computing faciltiy at the University of Dundee. You - will need a continuous network connection in order to use these services. - + Selecting one of the following menu items will start a remote service + on the high powered computing facility at the University of Dundee. You + will need a continuous network connection in order to use these services. +
Clustal Alignment

Clustal Realign

JPred