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:

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 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	featureType
Normally, 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