Sequence Features File
The Sequence features file (which used to be known as the "Groups file" prior to version 2.08) is a simple way of getting your own sequence annotations into Jalview. It was introduced to allow sequence features to be rendered in the Jalview applet, and so is intentionally lightweight and minimal because the applet is often used in situations where data file size must be kept to a minimum, and no XML parser is available.
Features files are imported into Jalview in the following ways:
-features <Features filename>
Sequence Features File Format
A features file is a simple ASCII text file, where each line contains tab separated text fields. No comments are allowed.
The first set of lines contain type definitions:
Feature label Feature Colour
A feature
type has a text label, and a colour (specified as a red,green,blue 24
bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
numbers (ranging from 0 to 255)). The text label may contain simple HTML
document body tags if enclosed by "<html></html>"
and will be rendered as formatted tooltips in the Jalview Application
(the Jalview applet is not capable of rendering HTML tooltips, so all
formatting tags will be removed.
The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences, optionally with some descriptive text (displayed in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a sequence, either by its text ID, or its index in an associated alignment.
description sequenceId sequenceIndex start end featureTypeNormally, sequence features are associated with sequences rather than alignments, and the sequenceIndex field is given as "-1". In order to specify a sequence by its index in a particular alignment, the sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the sequenceId field will be used in preference to the sequenceIndex field.
Feature annotations can be collected into named groups by
prefixing definitions with lines of the form:startgroup groupname
..
and subsequently post-fixing the group with:endgroup groupname
Feature
grouping was introduced in version 2.08, and used to control whether a
set of features are either hidden or shown together in the sequence Feature settings dialog box.
A complete example is shown below :
domain red metal ion-binding site 00ff00 transit peptide 0,105,215 chain 225,105,0 modified residue 105,225,35 signal peptide 0,155,165 helix ff0000 strand 00ff00 coil cccccc Your Own description here FER_CAPAA -1 3 93 domain Your Own description here FER_CAPAN -1 48 144 chain Your Own description here FER_CAPAN -1 50 140 domain Your Own description here FER_CAPAN -1 136 136 modified residue Your Own description here FER1_LYCES -1 1 47 transit peptide Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide Your Own description here Q93XJ9_SOLTU -1 49 144 chain startgroup secondarystucture PDB secondary structure annotation FER1_SPIOL -1 52 59 strand PDB secondary structure annotation FER1_SPIOL -1 74 80 helix endgroup secondarystructure