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:
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.
-After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview first determines if - the sequences are contained in Uniprot and then retrieves any sequence - records. This delay will normally only happen once for a particular - set of sequences, as jalview caches uniprot records in a file in your home - directory called '.jalview.uniprot.xml'. - -
The Sequence Identification Process - -
-The first step in the procedure for matching uniprot IDs to - sequences is to use the ID (name) of - each sequence to retrieve Uniprot records directly.
-- If a uniprot record (or set of records) is found for a sequence, - then the sequence is aligned to the one in the Uniprot record - to determine the correct start and end residue positions (which are - displayed when the 'Show Full Sequence ID' option is set). -
- -If the alignment reveals differences between the sequence in the - alignment and the one in the record, then Jalview will assume that - the aligned sequence is not the one in the uniprot record. - -
- -- In some cases, the ID used to retrieve Uniprot records may be out of - date and you will be notified of that a 100% match between the - 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.
+ 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. +
+ +