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.
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