Sequence Features File Format
-(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
-
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 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. + +
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 seuqence ID panel, and any embedded links can be accessed from the popup menu.
+
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 ++ + + +