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
-Note: This format is primarily intended to be used for the applet, which does - not have an XML parser and where file size must be kept to a minimum to reduce - download time.
-(Prior to version 2.08 known as the "Groups file")
- A precalculated Features file can read onto an alignment from the command line
- ("-features"), by drag and dropping the features file onto an alignment
- or by selecting from the File menu "Load Features / Annotations".
Specify the feature types first, then refer to the feature type for each sequence.
-featureType<tab>colour
- description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType
eg
- 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
- 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
An additional option in Jalview 2.08 is to group features in the following - way:
-STARTGROUP<tab>My feature groupA
- ....Many Feature descriptions here
- ENDGROUP<tab>My feature groupA
+
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 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 ++