Alignment Window Menus

From c554d41a4effc6719895bda6b3abc04c032715a8 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 26 Aug 2008 15:54:16 +0000 Subject: [PATCH] 2.4 release documentation update menus, service refs, new features and releases --- help/helpTOC.xml | 5 +- help/html/menus/alignmentMenu.html | 860 ++++++++++++++++++------------------ help/html/menus/alwcalculate.html | 6 + help/html/menus/wsmenu.html | 16 +- help/html/releases.html | 101 +++-- help/html/webServices/jnet.html | 6 +- help/html/whatsNew.html | 84 ++-- 7 files changed, 574 insertions(+), 504 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 75eb7df..9ad08fa 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -4,10 +4,9 @@ - - + - + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 22a0bd7..d2ca481 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,422 +1,438 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

File -

Fetch Sequence
- Shows a dialog window in which you can select known ids from - Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by - the European Bioinformatics Institute. See Sequence Fetcher.
Add Sequences
- Add sequences to the visible alignment from file, URL, or cut & - paste window
Reload
- Reloads the alignment from the original file, if available.
- Warning: This will delete any edits, analyses and - colourings applied since the alignment was last saved, and cannot be - undone.
Save (Control S)
- Saves the alignment to the file it was loaded from (if available), in - the same format, updating the original in place.
Save As (Control Shift S)
- 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.
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. The - output window also has a "New Window" - button to import the (possibly edited) text as a new alignment.
- Select the format of the text by selecting one of the following menu - items. -
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
-
Print (Control P)
- 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. -
Export Image
- Creates an alignment graphic with the current view's 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.
-
Export Features
- All features visible on the alignment can be saved to file or - displayed in a textbox in either Jalview or GFF format
Export Annotations
- All annotations visible on the alignment can be saved to file or - displayed in a textbox in Jalview annotations format.
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.
Load Features / Annotations
- Load files describing precalculated sequence features or alignment annotations.
Close (Control W)
- 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 (Control Z)
- 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 (Control Y)
- Any actions which you undo can be redone using redo.
Cut (Control X)
- 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 (Control C)
- 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 FASTA.
Paste -
- To New Alignment (Control Shift V)
  - A new alignment window will be created from sequences - previously copied or cut to the system clipboard.
  - Use <CTRL> and <SHIFT> and V(<APPLE> and - <SHIFT;> and and V on MacOSX) to paste.
- Add To This Alignment (Control V)
  - Copied sequences from another alignment window can be added - to the current Jalview alignment.
-
Delete (Backspace)
- This will delete the currently selected residues without - copying them to the clipboard. Like the other edit operations, this - can be undone with Undo.
Remove Left (Control L)
- 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 (Control R)
- 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 (Control E)
- All columns which only contain gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences.
Remove All Gaps (Control Shift E)
- 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 (Control D)
- 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
- When selected, the alignment will be kept at minimal width - (so there no empty columns before or after the first or last aligned - residue) and all sequences will be padded with gap characters to the - before and after their terminating residues.
- This switch is useful when making a tree using unaligned sequences and - when working with alignment analysis programs which require 'properly - aligned sequences' to be all the same length.
- You may set the default for Pad Gaps in the preferences.

Select -

Find... - (Control F)
- Opens the Find dialog box to search for residues, sequence name or - residue position within the alignment and create new sequence features - from the queries.
Select All (Control A)
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select - all.
Deselect All (Escape)
- 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 Sequence Selection (Control I)
- Any sequence ids currently not selected will replace the - current selection.
Invert Column Selection (Control Alt I)
- Any columns currently not selected will replace the current - column selection.
Undefine Groups (Control U)
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.

View -

New View (Control T)
- Creates a new view from the current alignment view.
Expand Views (X)
- Display each view associated with the alignment in its own alignment - window, allowing several views to be displayed simultaneously.
Gather Views (G)
- Each view associated with the alignment will be displayed within its - own tab on the current alignment window.
Show→(all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
Hide→(all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
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.
Show Sequence Features
- Show or hide sequence features on this alignment.
Seqence - Feature Settings...
- Opens the Sequence Feature Settings dialog box to control the - colour and display of sequence features on the alignment, and - configure and retrieve features from DAS annotation servers.

-
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.
-

-
Alignment Window Format Menu -
-
Font...
- Opens the "Choose Font" dialog box, in order to - change the font of the display and enable or disable 'smooth fonts' - (anti-aliasing) for faster alignment rendering.
-
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.
- Additional options for display of sequence numbering and scales are - also visible in wrapped layout mode:
-
-
Scale Above
- Show the alignment column position scale.
-
Scale Left
- Show the sequence position for the first aligned residue in each row - in the left column of the alignment.
-
Scale Right
- Show the sequence position for the last aligned residue in each row - in the right-most column of the alignment.
-
Show Sequence Limits
- 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
-
Right Align Sequence ID
- If this box is selected then the sequence names displayed in - the sequence label area will be aligned against the left-hand edge of - the alignment display, rather than the left-hand edge of the alignment - window.
-
Show Hidden Markers
- When this box is selected, positions in the alignment where - rows and columns are hidden will be marked by blue arrows.
-
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.
-
-
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 - Text...
- Opens the Colour Text dialog box to set a different text colour for - light and dark background, and the intensity threshold for transition - between them.
-
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.
-
-
By Annotation
- Colours the alignment on a per-column value from a specified - annotation. See Annotation - Colouring.
-
-
-
-
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.
-
-
Autocalculate Consensus
- For large alignments it can be useful to deselect - "Autocalculate Consensus" when editing. This prevents the - sometimes lengthy calculations performed after each sequence edit.
-
-
-
-
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.
-
MAFFT Multiple Sequence Alignment
- Submits all, or just the currently selected region for - alignment with MAFFT.
-
Muscle Multiple Protein Sequence Alignment
- Submits all, or just 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 in the set (that is, the one - that appears first in the alignment window).
-
-
-
-
-
- - + + +Alignment Window Menus + + + +
Alignment Window Menus
+
File +
+
Fetch Sequence
+ Shows a dialog window in which you can select known ids from + Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by + the European Bioinformatics Institute. See Sequence Fetcher.
+
Add Sequences
+ Add sequences to the visible alignment from file, URL, or cut & + paste window
+
Reload
+ Reloads the alignment from the original file, if available.
+ Warning: This will delete any edits, analyses and + colourings applied since the alignment was last saved, and cannot be + undone.
+
Save (Control S)
+ Saves the alignment to the file it was loaded from (if available), in + the same format, updating the original in place.
+
Save As (Control Shift S)
+ 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.
+
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. The + output window also has a "New Window" + button to import the (possibly edited) text as a new alignment.
+ Select the format of the text by selecting one of the following menu + items. +
+
FASTA
+
MSF
+
CLUSTAL
+
BLC
+
PIR
+
PFAM
+
+
+
Print (Control P)
+ 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. +
+
Export Image
+ Creates an alignment graphic with the current view's 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.
+
+
+
Export Features
+ All features visible on the alignment can be saved to file or + displayed in a textbox in either Jalview or GFF format
+
Export Annotations
+ All annotations visible on the alignment can be saved to file or + displayed in a textbox in Jalview annotations format.
+
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.
+
Load Features / Annotations
+ Load files describing precalculated sequence features or alignment annotations.
+
Close (Control W)
+ 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 (Control Z)
+ 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 (Control Y)
+ Any actions which you undo can be redone using redo.
+
Cut (Control X)
+ 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 (Control C)
+ 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 FASTA.
+
Paste +
+
To New Alignment (Control Shift V)
+ A new alignment window will be created from sequences + previously copied or cut to the system clipboard.
+ Use <CTRL> and <SHIFT> and V(<APPLE> and + <SHIFT;> and and V on MacOSX) to paste.
+
Add To This Alignment (Control V)
+ Copied sequences from another alignment window can be added + to the current Jalview alignment.
+
+
+
Delete (Backspace)
+ This will delete the currently selected residues without + copying them to the clipboard. Like the other edit operations, this + can be undone with Undo.
+
Remove Left (Control L)
+ 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 (Control R)
+ 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 (Control E)
+ All columns which only contain gap characters ("-", + ".") will be deleted.
+ You may set the default gap character in preferences.
+
Remove All Gaps (Control Shift E)
+ 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 (Control D)
+ 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
+ When selected, the alignment will be kept at minimal width + (so there no empty columns before or after the first or last aligned + residue) and all sequences will be padded with gap characters to the + before and after their terminating residues.
+ This switch is useful when making a tree using unaligned sequences and + when working with alignment analysis programs which require 'properly + aligned sequences' to be all the same length.
+ You may set the default for Pad Gaps in the preferences.
+
+
+
Select +
+
Find... + (Control F)
+ Opens the Find dialog box to search for residues, sequence name or + residue position within the alignment and create new sequence features + from the queries.
+
Select All (Control A)
+ Selects all the sequences and residues in the alignment.
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select + all.
+
Deselect All (Escape)
+ 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 Sequence Selection (Control I)
+ Any sequence ids currently not selected will replace the + current selection.
+
Invert Column Selection (Control Alt I)
+ Any columns currently not selected will replace the current + column selection.
+
Undefine Groups (Control U)
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
+
+
View +
+
New View (Control T)
+ Creates a new view from the current alignment view.
+
Expand Views (X)
+ Display each view associated with the alignment in its own alignment + window, allowing several views to be displayed simultaneously.
+
Gather Views (G)
+ Each view associated with the alignment will be displayed within its + own tab on the current alignment window.
+
Show→(all Columns / Sequences)
+ All hidden Columns / Sequences will be revealed.
+
Hide→(all Columns / Sequences)
+ Hides the all the currently selected Columns / Sequences
+
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.
+
Show Sequence Features
+ Show or hide sequence features on this alignment.
+
Seqence + Feature Settings...
+ Opens the Sequence Feature Settings dialog box to control the + colour and display of sequence features on the alignment, and + configure and retrieve features from DAS annotation servers.
+
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.
+
+
+
Alignment Window Format Menu +
+
Font...
+ Opens the "Choose Font" dialog box, in order to + change the font of the display and enable or disable 'smooth fonts' + (anti-aliasing) for faster alignment rendering.
+
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.
+ Additional options for display of sequence numbering and scales are + also visible in wrapped layout mode:
+
+
Scale Above
+ Show the alignment column position scale.
+
Scale Left
+ Show the sequence position for the first aligned residue in each row + in the left column of the alignment.
+
Scale Right
+ Show the sequence position for the last aligned residue in each row + in the right-most column of the alignment.
+
Show Sequence Limits
+ 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
+
Right Align Sequence ID
+ If this box is selected then the sequence names displayed in + the sequence label area will be aligned against the left-hand edge of + the alignment display, rather than the left-hand edge of the alignment + window.
+
Show Hidden Markers
+ When this box is selected, positions in the alignment where + rows and columns are hidden will be marked by blue arrows.
+
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.
+
Centre Annotation Labels
+ Select this to center labels along an annotation row + relative to their associated column (default is off, i.e. left-justified).
+
+
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 + Text...
+ Opens the Colour Text dialog box to set a different text colour for + light and dark background, and the intensity threshold for transition + between them.
+
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.
+
+
By Annotation
+ Colours the alignment on a per-column value from a specified + annotation. See Annotation + Colouring.
+
+
+
+
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.
+
+
Extract Scores ... (optional)
+ This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
+ When selected, these numbers are parsed into sequence associated annotation which can + then be used to sort the alignment via the Sort by→Score menu.
+
+
Autocalculate Consensus
+ For large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This prevents the + sometimes lengthy calculations performed after each sequence edit.
+
+
+
+
Web Service
+ +
Fetch DB References
+ This will use any of the database services that Jalview is aware + of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI) + to verify the sequence and retrieve all database cross references and PDB ids + associated with all or just the selected sequences in the alignment.
+
+
+ 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.
+
MAFFT Multiple Sequence Alignment
+ Submits all, or just the currently selected region for + alignment with MAFFT.
+
Muscle Multiple Protein Sequence Alignment
+ Submits all, or just 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 in the set (that is, the one + that appears first in the alignment window).
+
+
+
+
+
+ + diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 6ee7ed8..700ce51 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -45,6 +45,12 @@ in the alignment. See Principal Component Analysis.

+
Extract Scores ... (optional)
+ This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
+ When selected, these numbers are parsed into sequence associated annotation which can + then be used to sort the alignment via the Sort by→Score menu.
+
+
Autocalculate Consensus
For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index a1df34a..7ee893b 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -3,16 +3,18 @@
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.

Fetch DB References
- This will use the service WSDBFetch, provided by the EBI, to retrieve all - uniprot database cross references and PDB ids associated with the selected sequences in - the alignment if the sequences have valid Uniprot names or accession ids.
+ This will use any of the database services that Jalview is aware + of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI) + to verify the sequence and retrieve all database cross references and PDB ids + associated with all or just the selected sequences in the alignment.

+
+ 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
diff --git a/help/html/releases.html b/help/html/releases.html index 2f340ff..a7f6cfd 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -19,35 +19,52 @@
2.4
- Feb/2008
+ 27/8//2008 -
-
New VAMSAS capabilities in Jalview + User Interface
-
treenode binding for VAMSAS tree exchange
-
local editing and update of sequences in VAMSAS alignments - (experimental)
-
Create new or select existing session to join
-
load and save of vamsas documents
-
-
-
Retrieval of cross-referenced sequences from other databases -
-
export annotation rows as CSV for spreadsheet import
-
Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings

Linked highlighting of codon and amino acid from translation and protein products
+
Linked highlighting of structure associated with residue mapping to codon position
+
Sequence Fetcher provides example accession numbers and 'clear' button
+
MemoryMonitor added as an option under Desktop's Tools menu
+
Extract score function to parse whitespace separated numeric data in description line
+
Column labels in alignment annotation can be centred.
+
Tooltip for sequence associated annotation give name of sequence
+
+ Web Services and URL fetching +

JPred3 web service
-
Generalised database reference retrieval and validation to - all fetchable databases
-
Fetch sequences from DAS sources supporting the sequence command
+
Prototype sequence search client (no public services available yet)

Fetch either seed alignment or full alignment from PFAM
-
Sequence Fetcher GUI provides example accession numbers and 'clear' button

URL Links created for matching database cross references as well as sequence ID

URL Links can be created using regular-expressions
-
Application command line +
+ Sequence Database Connectivity +
+
Retrieval of cross-referenced sequences from other databases +
+
Generalised database reference retrieval and validation to + all fetchable databases
+
Fetch sequences from DAS sources supporting the sequence command
+
+ Import and Export +
export annotation rows as CSV for spreadsheet import
+
Jalview projects record alignment dataset associations, EMBL + products, and cDNA sequence mappings
+
Sequence Group colour can be specified in Annotation File
+
Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme
+
+ VAMSAS Client capabilities (Experimental) +
+
treenode binding for VAMSAS tree exchange
+
local editing and update of sequences in VAMSAS alignments + (experimental)
+
Create new or select existing session to join
+
load and save of vamsas documents
+
+ Application command line

-tree parameter to open trees (introduced for passing from applet)
@@ -58,33 +75,27 @@
-groovy command line argument executes a given groovy script after all input data has been loaded and parsed

-
-
Trees passed as applet parameters can be passed to + Applet-Application data exchange +
+
Trees passed as applet parameters can be passed to application (when using "View in full application")
-
MemoryMonitor added as an option under Desktop's Tools menu -
-
allow reading of JPred concise files as a normal filetype
-
sort sequences by named annotation scores
-
Re-instated Full AMSA support and .amsa file association
-
Stockholm annotation parsing and alignment properties import -
-
Applet Parameters +
+ Applet Parameters

feature group display control parameter

debug parameter

showbutton parameter

-
-
Applet API methods + Applet API methods

newView public method

Window (current view) specific get/set public methods

Feature display control methods
+
get list of currently selected sequences

-
-
- New Jalview distribution features + New Jalview distribution features
+
InstallAnywhere Installer upgraded to IA 2008 VP1

RELEASE file gives build properties for the latest Jalview release.

Java 1.1 Applet build made easier and donotobfuscate @@ -93,9 +104,9 @@
Debug flag for javacc

.jalview_properties file is documented (slightly) in jalview.bin.Cache
-
Group colour can be given as an RGB triplet which is used to colour all non-gap characters
- +
Continuous Build Integration for stable and development version of Application, Applet and source distribution

+
@@ -120,6 +131,7 @@
better reporting of non-fatal warnings to user when file parsing fails.

Save works when Jalview project is default format
+
Save as dialog opened if current alignment format is not a valid output format

Uniprot canonical names introduced for both das and vamsas

Histidine should be midblue (not pink!) in Zappo

error messages passed up and output when data read fails
@@ -127,6 +139,10 @@ is edited
allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly
+
allow reading of JPred concise files as a normal filetype
+
Stockholm annotation parsing and alignment properties import fixed for PFAM records +
+
Structure view windows have correct name in Desktop window list

annotation consisting of sequence associated scores can be read and written correctly to annotation file

Aligned cDNA translation to aligned peptide works correctly @@ -140,7 +156,18 @@
Secondary structure lines are drawn starting from first column of alignment

Uniprot XML import updated for new schema release in July 2008
+
Sequence feature to sequence ID match for Features file is case-insensitive
+
Sequence features read from Features file appended to all sequences with matching IDs
+
PDB structure coloured correctly for associated views containing a sub-sequence
+
PDB files can be retrieved by applet from Jar files
+
feature and annotation file applet parameters referring to different directories are retrieved correctly
+
Fixed application hang whilst waiting for splash-screen version check to complete
+
Applet properly URLencodes input parameter values when passing them to the launchApp service
+
display name and local features preserved in results retrieved from web service
+
Visual delay indication for sequence retrieval and sequence fetcher initialisation
+
updated Application to use DAS 1.53e version of dasobert DAS client
+
Re-instated Full AMSA support and .amsa file association

diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index a8727db..114fc33 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -10,7 +10,11 @@ composition and similarity to sequences with known secondary structure. The JNet method uses several different neural networks and decides on the most likely prediction via a jury network.

-
Cuff J. A and Barton G.J (1999) Application of enhanced +
+ 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

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 98f01dc..a090673 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -4,46 +4,62 @@
What's new ?
-
Jalview Version 2.4
+
Highlights in Jalview Version 2.4

- VAMSAS Interoperation Client
- DAS Sequence Fetching
+ DNA and protein product highlighting
+ URL links generated with regular expressions
+ URL links for sequence database cross references
+ New sequence fetcher dialog and DAS Sequence Fetching
+ JPred Service upgraded to Jpred3
+ Memory monitor
PFAM full alignment retrieval
- DNA/Protein Product traversal (Experimental)
- .. (more to come)
- URL links can be generated using regular - expressions and created for sequence database cross references
+ Generalised sequence database reference validation
+ DNA Protein Product sequence db traversal (Experimental)
+ VAMSAS Interoperation Client (Experimental)
+ export annotation rows as CSV for spreadsheet import
+ New application command line args and optional Groovy suport
+ New Applet API methods and parameters

-
Issues Resolved
+
Issues Resolved (a select list)

- .. (more to come) + Aligned cDNA translation to aligned peptide works correctly
+ selected region output includes visible annotations (for + certain formats)
+ edit label/displaychar contains existing label/char for + editing
+ Newick tree support improved for clustalW trees and preserving NHX style comments
+ Pathological filechooser bug avoided by not allowing + filenames containing a ':'
+ Fixed exception when parsing GFF files containing global + sequence features
+ Reference counting for alignment datasets
+ better reporting of non-fatal warnings and error messages to user when file + parsing fails.
+ Save works when Jalview project is default format
+ Histidine should be midblue (not pink!) in Zappo
+ Undo recovers dataset sequence metadata when sequence + regions are cut
+ PDB files without pdb ID HEADER lines (like those + generated by MODELLER) are read in properly
+ Stockholm annotation parsing fixed and improved (PFAM records)
+ Re-instated Full AMSA support and .amsa file association (MyHits)
+ annotation consisting of sequence associated scores can be + read and written correctly to annotation file
+ Fixed display of hidden sequence markers and non-italic font + for representatives in Applet
+ Applet Menus are always embedded in applet window on Macs.
+ Newly shown features appear at top of stack (in Applet)
+ Secondary structure lines are drawn starting from first + column of alignment
+ Uniprot XML import updated for new schema release in July 2008
+ Sequence feature to sequence ID match for Features file is case-insensitive
+ Sequence features read from Features file appended to all sequences with matching IDs
+ PDB structure coloured correctly for associated views containing a sub-sequence
+ Display name and local features preserved in results retrieved from web service
+ Visual delay indication for sequence retrieval and sequence fetcher initialisation
+ Updated Application to use DAS 1.53e version of dasobert DAS client
-<--
Jalview Version 2.3
-
- Jmol 11.0.2 integration
- PDB views stored in Jalview XML files
- Slide sequences
- Edit sequence in place
- EMBL CDS features
- DAS Feature mapping
- Feature ordering
- Alignment Properties
- Annotation Scores
- Sort by scores
- Feature/annotation editing in applet
-
-
Issues Resolved
-
- Headless state operation in 2.2.1
- Incorrect and unstable DNA pairwise alignment
- Cut and paste of sequences with annotation
- Feature group display state in XML
- Feature ordering in XML
- 2.2.1 applet had no feature transparency
- Number pad keys can be used in cursor mode
- Structure Viewer mirror image resolved
-
-->

See the Release History page for details of all new features and resolved issues.
-- 1.7.10.2