Sequence Features
-This displays Uniprot sequence features on the alignment if a 100% sequence - match is found.
-The first step in this process is to match the id (name) of each sequence with - Uniprot. If there is no match, a Blast search is performed to try to obtain - the Uniprot Id for each sequence. You will be notified of any 100% matches with - Uniprot, which you must manually assign to each sequence in your input alignment, - then save the file.
-- The input sequence will be matched with the returned Uniprot record, the start - and end residues can then be correctly assigned to each sequence.
-Sequence features which are 1 residue in length are coloured red. Features - which span a region are coloured blue.
-By moving the mouse pointer over a sequence feature on the alignment a small - label will appear with the description of that sequence feature.
-A local cache of retrieved uniprot entries is recorded on your local machine. -
- - + + + ++ 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. +
+ +