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
-