Alignment Conservation Annotation

From: amwaterhouse Date: Tue, 4 Apr 2006 17:07:14 +0000 (+0000) Subject: Modified for 2.08 X-Git-Tag: Release_2_08~66 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8c0737632c158907098990b81ac702710721e9f2;p=jalview.git Modified for 2.08 --- diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index cf7faf5..4cfc825 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,27 +1,27 @@ - -Alignment Conservation Annotation -

Alignment Conservation Annotation

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

CABIOS

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

- -

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

- - + +Alignment Conservation Annotation +

Alignment Conservation Annotation

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

CABIOS

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

+ +

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

+ + diff --git a/help/html/editing/index.html b/help/html/editing/index.html index 734a662..8ff1cf6 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -2,6 +2,20 @@ Editing

Editing

Jalview 2.08 Enhancements - Editing can be restricted to the current + selection area. This allows the user to "Lock" the alignment either + side of the selection area. Any gap insertions or deletions will only affect + the current selection area.

In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, + the same number of gaps will be inserted at position 116, (between M and L). +

Editing is possible via the keyboard by toggling the Cursor mode on / off with + F2. A full list of keyboard editing actions is found here. +

Tip: For large alignments, deselect "Calculate -> + Autocalculate Consensus" to prevent the alignment performing lengthy calculations + after every edit.

Inserting / removing gaps - hold down the "Shift" key. Click a residue with the mouse and drag the residue to the right to insert gaps or to the left to remove gaps.
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 3ad7f3e..3635bbe 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -3,34 +3,37 @@

Alignment Annotation

In addition to the definition of groups, Jalview also allows you to -mark particular columns of an alignment and add symbols and text in -the annotation area shown below the alignment (which may be hidden if -View→Show Annotation is not ticked). -

In addition to the definition of groups, Jalview also allows you to mark particular + columns of an alignment and add symbols and text in the annotation area shown + below the alignment (which may be hidden if View→Show Annotation + is not ticked).

As of Jalview 2.08 precalculated annotations can be added to alignments from + the command line, drag and drop, or from the "File-> Load Features / + Annotations" menu item. See the Annotations + File Format for more details.

Annotation rows are added using the Annotation Label menu, which is obtained 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. -

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. +

Editing Label and secondary structure Annotation

Jalview Archives

Jalview Project Archives -

These are java archives of an XML file containing alignments, trees -and Jalview display information. A data exchange standard is currently -being developed, so there is no stable schema yet, but Jalview web -services will soon make use of the same interchange format.

Jalview Archives

Jalview Project Archives +

These are java archives of an XML file containing alignments, trees and Jalview + display information. A data exchange standard is currently being developed, + so there is no stable schema yet, but Jalview web services will soon make use + of the same interchange format.

For those who want to know...
+ Jalview uses java classes automatically created using Castor. + Jalview 2.08 uses descriptor classes which significantly increase the speed + of marshalling / unmarshalling java objects into XML. Files created prior to + Jalview 2.08 can still be read in, but they will be saved in the new format. +

Full Sequence ID - If selected the ID panel will display the name of a sequence plus the start and end residues in the format name/start-end. If not selected, the displayed ID will be the name of the sequence.

Font - The default font name, size and style can be set for a new alignment - window.

Font - The default font name, size and style can be set for a new + alignment window.

Smooth Font - Toggles anti-aliasing on / off for faster rendering + of the alignment.

Gap Symbol - The default gap symbol may be set to either "-" or "."

Colour - The default colour scheme for a new alignment window. If the chosen option is "User Defined" then the last User Defined Colour diff --git a/help/html/features/search.gif b/help/html/features/search.gif index c7b114a..d571085 100755 Binary files a/help/html/features/search.gif and b/help/html/features/search.gif differ diff --git a/help/html/features/search.html b/help/html/features/search.html index 532fcb4..21126a1 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -13,12 +13,14 @@ td {

Search

The search box is displayed by pressing Control and F or selecting "Find..." from the "Search" menu.

"Find next" will find the next occurence of the specified - and adjust the alignment window view to show it, and "Find - all" highlights all matches for a pattern. The "Create new - group" is a quick way to highlight and group residues matching - the specified search pattern throughout the alignment.

"Find next" will find the next occurence of the specified and adjust + the alignment window view to show it, and "Find all" highlights all + matches for a pattern. The "New Feature" is a quick way to highlight + and group residues matching the specified search pattern throughout the alignment. + If "New Feature" is selected, the feature can be given a name from + a popup input box. Use the "Feature Settings" under the "View" + menu to change the visibility and colour of the new sequence feature.

The search uses regular expressions. (understands a mixture of posix and perl style regex - see below for a summary)

Sequence Features

View→Sequence Features

View→Fetch Sequence Features

When this option is selected, sequence features extracted from the Uniprot record for each sequence are displayed on the alignment.

Jalview will attempt to retrieve sequence features from Uniprot files using the EBI dbFetch web service using the given sequence names. A 100% match with the Uniprot record is required to view the Sequence Features.

More information about the feature is given in a tooltip, which is - viewed by moving the mouse pointer over a sequence feature. The - description associated with the feature will then be displayed in a small - label near the pointer.

More information about the feature is given in a tooltip, which is viewed by + moving the mouse pointer over a sequence feature. The description associated + with the feature will then be displayed in a small label near the pointer.

View→Show Sequence Features

Select whether to view the sequence features added to this alignment or not.

View→Feature Settings...

Once sequence features have been loaded onto an alignment features can be hidden or have their rendering priority changed using the Feature Settings dialog. @@ -49,10 +50,14 @@ sequence and a Uniprot record was identified, but the sequence name must be manually changed (by right clicking on the sequence ID and selecting Sequence→Edit Name), before Jalview will show its sequence - features.

remember to save your alignment if you have updated any of the - sequence IDs! -

remember to save your alignment if you have updated any of the sequence + IDs!

Precalculated Sequence Features may be added to an alignment from the command + line, drag and drop, or from the "File->Load Features / Annotations" + menu item. See the Features File Format for + more details.

Control 'F' - Launches the search window.

Up Arrow - Moves selected sequence(s) up the alignment

Down Arrow - Moves selected sequence(s) down the alignment.

F1 - Show Help Documentation

F2 - Toggle Cursor mode on / off

With Cursor mode on....

Cursor keys - Move cursor around the alignment.

Space - Insert a gap at the cursor position.
+ To insert 12 spaces at the current cursor, type 12 before pressing Space.
+ To group insert, hold control or shift together with space.

Delete - Delete a gap at the cursor position.
+ To delete 12 spaces at the current cursor, type 12 before pressing Delete.
+ To group delete, hold down control or shift together with Delete.

S - Type a number x then press 'S' to jump to sequence x.

C - Type a number x then press 'C' to jump to column x.

P - Type a number x then press 'P' to jump to position x in current sequence.

Q - Define the top left corner of the selection area

M - Define the bottom right corner of the selection area

Load Features / Annotations
+ Jalview load precalculated sequence + features or alignment + annotations.
Close
Close the alignment window. Make sure you have saved your alignment before you close - either as a Jalview project or by using the diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 97bff22..5a97296 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -45,6 +45,11 @@ in the alignment. See Principal Component Analysis.
Autocalculate Consensus
+ For large alignments it can be useful to deselect "Autocalculate + Consensus" when editing. This prevents lengthy calculations which are + performed after each sequence edit.
+

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.

-
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 +
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 + 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!
+ 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 + 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.
+ 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.
+

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 6088546..9be2775 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -10,7 +10,13 @@

Font
Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
+ dialog box, which is shown when this item is selected. Select a "Monospaced" + font for fast rendering of your alignment. The checkbox labelled "Monospaced" + indicates whether the chosen font uses characters all of the same width.
+
+
Smooth Fonts
+ If selected, the alignment will be drawn with anti-aliasing on which looks + better, but performace is reduced.

Wrap
When ticked, the alignment display is "wrapped" @@ -63,7 +69,7 @@
Seqence Settings
If features have been added to the alignment then the priority of rendering the features can be altered so that overlapping features can be displayed - or hidden. See Sequence Features.
+ or hidden. See Sequence Features.

Overview Window
A scaled version of the alignment will be displayed in a small diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index fd65178..d4b8b5f 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -42,10 +42,11 @@ This menu is only visible if you right-click on a sequence name.
-
Edit Name
- You may edit the name of each sequence. A window will be - displayed asking for a new sequence name to be entered. Press OK to accept - your edit.
+
Edit Name/Description
+ You may edit the name and description of each sequence. A + window will be displayed asking for a new sequence name and sequence description + to be entered. Press OK to accept your edit. To save sequence descriptions, + you must save in Fasta, PIR or Jalview File format.

View PDB Structure
diff --git a/help/html/releases.html b/help/html/releases.html index 8c101b9..70c7b4d 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -4,9 +4,28 @@
Release History
- - - + + + + + + + + -

Release
New Features
Issues Resolved
Release
New Features
Issues Resolved
2.08
+ 6/4/06
+
Editing can be locked to selection area
+
Keyboard editing
+
Create sequence features from Searches
+
Precalculated annotations can be loaded onto alignments
+
Features file allows grouping of features
+
Annotation Colouring scheme added
+
Smooth fonts off by default - Faster rendering
+
Choose to toggle Autocalculate Consensus On/Off
+
+
Drag & Drop fixed on Linux
+
Jalview Archive file faster to load/save, sequence descriptions saved. +
+

2.07
@@ -38,8 +57,7 @@

-
2.05b
+

2.05b
15/9/05

Choose EPS export as lineart or text
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 7bc6de4..5a3ed19 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,28 +2,32 @@ What's new ?
What's new ?
-
Jalview Version 2.07
-
Sequence Fetcher has been added to quickly - retrieve sequences with known ids from several databases.
-
Sequence Features enhanced to allow - the user to display all features of a Uniprot file on the alignment and subsequently - colour, hide or show overlapping features.
-
Choose to omit /start-end from sequences when - saving files. This is important for saving files to be used by some programs - which cannot read the original Jalview sequence output with the appended /start-end.
-
PDB structure viewer enhanced. Mapping - between sequence and structure has been enhanced, colours on the alignment are - reflected in the structure viewer.
-
Jalview Applet can read - in feature files, PDB files be used as input to HTML form See the website - to find out the new parameters available for the Applet Version of Jalview.
-

+
Jalview Version 2.08
+
Editing can be locked to selection area. + Any edits made within the locked area do not affect the rest of the alignment.
+
Keyboard editing - press F2 to toggle Cursor mode On / Off. For a full list + of keyboard controls, look here.
+
Create sequence features from Searches. + Previously results from searches were added as alignment positions, which was + wrong. Now the search results are saved as sequence features and their visibility + and colour can be modified using the Sequence + Feature Settings window.
+
Precalculated annotations can be loaded onto alignments. The Annotation + File format is a tab delimited set of values.
+
Features file allows grouping of + features. The Sequence Feature Settings + window then makes it very easy to set the visibility of groups of features. +
+
Annotation Colouring + scheme added. A new colour scheme which colours columns on a per-column value.
+
Smooth fonts off by default - Faster rendering. Toggle on / off from the View + menu, or can be set in Preferences.
+
Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.
+

Issues Resolved
-
Group Editing is possible with Control and mouse click. Alt key and mouse press - does not work as this translates as the middle mouse button, which since 2.04 - is now used to scroll the alignment and change the font size.
-
HTML export now writes groups and features which were previously missing.
-

+
Drag & Drop fixed on Linux
+
Jalview Archive file faster to load/save, sequence descriptions saved.
+

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

Release	New Features	Issues Resolved	Release	New Features	Issues Resolved
2.08 + 6/4/06	+ Editing can be locked to selection area + Keyboard editing + Create sequence features from Searches + Precalculated annotations can be loaded onto alignments + Features file allows grouping of features + Annotation Colouring scheme added + Smooth fonts off by default - Faster rendering + Choose to toggle Autocalculate Consensus On/Off +	+ Drag & Drop fixed on Linux + Jalview Archive file faster to load/save, sequence descriptions saved. + +
2.07 @@ -38,8 +57,7 @@
- 2.05b +	2.05b 15/9/05	Choose EPS export as lineart or text diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 7bc6de4..5a3ed19 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,28 +2,32 @@ What's new ? What's new ? - Jalview Version 2.07 - Sequence Fetcher has been added to quickly - retrieve sequences with known ids from several databases. - Sequence Features enhanced to allow - the user to display all features of a Uniprot file on the alignment and subsequently - colour, hide or show overlapping features. - Choose to omit /start-end from sequences when - saving files. This is important for saving files to be used by some programs - which cannot read the original Jalview sequence output with the appended /start-end. - PDB structure viewer enhanced. Mapping - between sequence and structure has been enhanced, colours on the alignment are - reflected in the structure viewer. - Jalview Applet can read - in feature files, PDB files be used as input to HTML form See the website - to find out the new parameters available for the Applet Version of Jalview. - + Jalview Version 2.08 + Editing can be locked to selection area. + Any edits made within the locked area do not affect the rest of the alignment. + Keyboard editing - press F2 to toggle Cursor mode On / Off. For a full list + of keyboard controls, look here. + Create sequence features from Searches. + Previously results from searches were added as alignment positions, which was + wrong. Now the search results are saved as sequence features and their visibility + and colour can be modified using the Sequence + Feature Settings window. + Precalculated annotations can be loaded onto alignments. The Annotation + File format is a tab delimited set of values. + Features file allows grouping of + features. The Sequence Feature Settings + window then makes it very easy to set the visibility of groups of features. + + Annotation Colouring + scheme added. A new colour scheme which colours columns on a per-column value. + Smooth fonts off by default - Faster rendering. Toggle on / off from the View + menu, or can be set in Preferences. + Choose to toggle Autocalculate Consensus On/Off from the Calculate menu. + Issues Resolved - Group Editing is possible with Control and mouse click. Alt key and mouse press - does not work as this translates as the middle mouse button, which since 2.04 - is now used to scroll the alignment and change the font size. - HTML export now writes groups and features which were previously missing. - + Drag & Drop fixed on Linux + Jalview Archive file faster to load/save, sequence descriptions saved. + See the Release History page for details of all new features and resolved issues.