Sequence Features File

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:

from the command line
```
 -features <Features filename>
```
Dragging a features file onto an alignment window
Via the "Load Features / Annotations" entry in the File menu of an alignment window.

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 specification. This can be either:

A single colour specified as either a red,green,blue 24 bit triplet in hexadecimal (eg. 00ff00) or as comma separated numbers (ranging from 0 to 255))
A graduated colourscheme specified as a "|" separated list of fields:
```
[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
```
The fields are as follows:
- label
  Indicate that the feature description should be used to create a colour for features of this type.
  Note: if no threshold value is needed then the final '|' may be omitted.
  This keyword was added in Jalview 2.6
- mincolor and maxcolor
  Colour triplets specified as hexadecimal or comma separated values (may be left blank for a label style colourscheme, but remember to specify the remaining fields)
- absolute
  An optional switch indicating that the minvalue and maxvalue parameters should be left as is, rather than rescaled according to the range of scores for this feature type.
- minvalue and maxvalue
  Minimum and maximum values defining the range of scores for which the colour range will be defined over. If minvalue is greater than maxvalue then the linear mapping will have negative gradient.
- thresholdtype
  Either "none", "below", or "above". below and above require an additional threshold value which is used to control the display of features with a score either below or above the value.

The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences. Each feature can optionally include some descriptive text which is displayed in a tooltip when the mouse is near the feature on that sequence (and can also be used to generate a colour the feature).

If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or GFF3 (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, then you can leave it as is, after first adding a line containing only 'GFF' after any Jalview feature colour definitions (this mixed format capability was added in Jalview 2.6). Alternately, you can use Jalview's own sequence feature annotation format, which additionally allows HTML and URLs to be directly attached to each piece of annotation.

Jalview's sequence feature annotation format

Each feature is specified as a tab-separated series of columns as defined below:

description	sequenceId	sequenceIndex	start	end	featureType	score (optional)

This format allows two alternate ways of referring to a sequence, either by its text ID, or its index (base 0) in an associated alignment. 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.

The description may contain simple HTML document body tags if enclosed by "<html></html>" and these 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).
Attaching Links to Sequence Features
Any anchor tags in an html formatted description line will be translated into URL links. A link symbol will be displayed adjacent to any feature which includes links, and these are made available from the links submenu of the popup menu which is obtained by right-clicking when a link symbol is displayed in the tooltip.
Non-positional features
Specify the start and end for a feature to be 0 in order to attach it to the whole sequence. Non-positional features are shown in a tooltip when the mouse hovers over the sequence ID panel, and any embedded links can be accessed from the popup menu.
Scores
Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in Jalview 2.5). The score field is optional, and malformed scores will be ignored.

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
GFF
FER_CAPAA	GffGroup	domain	3	93	.	.