X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=fdaa0233478ea7509f25278b8f387d8b0ec88dcb;hb=1b9fc500a75a38d7c4408d4b209384d5236911cc;hp=ff741397db866eaf474431995df901a6b93c4d2f;hpb=1984126973e19bd10f39bb516d728c9226f2ba71;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ff74139..fdaa023 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,20 +1,21 @@
Alignment Window Menus
@@ -28,8 +29,8 @@
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
+ dialog window in which you can retrieve known ids from Uniprot,
+ EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
European Bioinformatics Institute. See Sequence Fetcher .
- Add Sequences
Add
@@ -235,17 +236,21 @@
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.
-
- - Make Groups
The currently
+ - Create Group (Control G)
+ Create a group containing the currently selected sequences.
+ - Remove Group (Shift Control G)
+ Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)
+ - Make Groups for selection
The currently
selected groups of the alignment will be subdivided according to
the contents of the currently selected region.
Use this to
subdivide an alignment based on the different combinations of
residues observed at specific positions. (new in jalview 2.5)
-
+ Undefine Groups (Control U)
The
+ alignment will be reset with no defined groups.
WARNING:
+ This cannot be undone.
+
+
View
- New View (Control T)
@@ -287,9 +292,13 @@
- Show Consensus Histogram
Enable or disable the display of the histogram above the
consensus sequence.
- - Show Consensus Profile
Enable
- or disable the display of the sequence logo above the consensus
+ - Show Consensus Logo
Enable
+ or disable the display of the Consensus Logo above the consensus
sequence.
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
- Group Conservation
When
ticked, display a conservation row for all groups (only available
for protein alignments).
@@ -391,6 +400,9 @@
+
+
+
Colour
@@ -407,7 +419,7 @@
Colour Scheme options: None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, User Defined
See
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
See
colours for a
description of all colour schemes.
By Conservation
See Annotation
Colouring.
+ By RNA Helices
+ Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ RNA Helices
+ Colouring.
+
Calculate
@@ -467,14 +484,15 @@
- Neighbour Joining Using Blosum62
+ Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.
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
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See Principal
Component Analysis.
Extract Scores ... (optional)
This
@@ -492,28 +510,36 @@
Sort With New Tree
When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.
-
+ Show Flanking Regions
Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides.
+
Web Service Menu
This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:
- 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.
'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.
- - Envision2 Services
Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the EnVision2 web
- application. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- ENFIN.
+ submenu contains options for accessing 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 sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+ - 'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment.
Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !
Added in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<
+
Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or