Sequence Features

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfeatures.html;h=fe8de4ec93c723c1695e17debfd5b9486a36599e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=4026071ed64c7fc7b04e08efa26cbbb5ab672195;hpb=92ae1457a784553ccdb842b122d481ce6c5ff24f;p=jalview.git diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 4026071..fe8de4e 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -1,43 +1,82 @@ - -Sequence Features - -

View→Sequence Features

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

Currently, sequence features are rendered in red or blue, dependent - upon their type:

Features associated with a particular residue are coloured - red
e.g. an active site residue
Features which span a region are coloured blue
-e.g. a region of sequence with known structure
-
More information about the feature is given in a tooltip, which are - viewed by moving the mouse pointer over a sequence feature. The - associated text for the feature will then be displayed in a small - label will appear near the pointer.
-
After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview must first determine if a - sequence is contained in uniprot and then retrieve its sequence - record. This delay should only happen once for a particular - alignment, as jalview caches uniprot records in a file in your home - directory called '.jalview.uniprot.xml'. - -
The first step in this process is to try to use the ID (name) of - each sequence as an ID search in Uniprot. If there is no match, The - EBI Blast search is used in an attempt to obtain the Uniprot Id for - each sequence. You will be notified of any 100% matches with - Uniprot, but you must then manually change the name of the sequence, - 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! -
-
- If a uniprot record (or set of records) is found for a sequence, - then the sequence in aligned to the one in the Uniprot record - to determine the correct start and end residue positions that will be - displayed when the 'Show Full Sequence ID' option is set.
- - + + + +Sequence Features + + +
Sequence Features
+
Jalview can colour parts of a sequence based on the presence of +sequence features - which may be retrieved from database records (such +as Uniprot), the result of sequence motif +searches or simply read from a sequence +features file. You can also create +features from the results of searches or the current selection, and edit features by double clicking on +them.
+
Sequence Feature Colouring Styles
+
By default, Jalview will assign a color to each feature based on +its type. These colours can be changed from the feature settings and amend features dialog boxes. Since +Jalview 2.5, it is also possible to define feature +colourschemes to shade features based on their associated scores or text +labels.
+
Sequence Feature Groups
+
Since Jalview 2.08, sequence features assigned to a sequence can +be organised into groups, which may indicate that the features were all +retrieved from the same database (such as Uniprot features), or +generated by the same analysis process (as might be specified in a sequence features file).
+
Sequence Feature Inheritance
+
Since Jalview 2.08, sequence features are global to a +set of sequences appearing (independently or together) in many different +alignments. Practically, this means features loaded onto one alignment +can be viewed in any alignments involving the same sequences. The same +sequence appears in different alignments when a new alignment is +generated by submitting an existing set of sequences to one of the +alignment or prediction web services, and when sequences are copied and +pasted into other alignment windows.
+
View→Show Sequence Features
+
Toggle the display of sequence features in this alignment. If +feature retrieval has not already been carried out, then Jalview will +automatically try to fetch sequence features (as described below).
+
View→Sequence Feature Settings...
+
Once sequence features have been loaded, their display can be +fully controlled using the alignment window's Sequence Feature Settings dialog box. +Feature colour schemes and display parameters are unique to a particular +alignment, so it is possible to colour the same sequence features +differently in different alignment views.
+Since Jalview 2.1, it is possible to add DAS +features to an alignment via the DAS tabbed pane of the feature settings +window.
+
View→Sequence ID Tooltip→Show +Non-Positional features
+Only available in application
+
+
Toggles the display of non-positional features in the sequence ID +tooltip, and whether they will be included when sequence features are +exported using "File→Export Features".
+
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.
+ +