[Jalview-discuss] Alignment Annotation File - SEQUENCE_REF format

Steffen Schmidt steffen.schmidt at tuebingen.mpg.de
Wed Jan 15 10:23:29 GMT 2014


Hi,

I your manual about annotation files you describe:
http://www.jalview.org/help/oldhelp/html/features/annotationsFormat.html

...
You can associate an annotation with a sequence by preceding its definition with the line:

SEQUENCE_REF	seq_name	[startIndex]
...

I wonder what the exact format of seq_name is:

Image I get a fasta file like this:
> db|183474|my_pet_protein

Do I have to put in the full id or are  other variations ok?

SEQUENCE_REF	db|183474|my_pet_protein	1
SEQUENCE_REF	183474	1
SEQUENCE_REF	my_pet_protein	1

Background: Since most often accession numbers don’t tell you the species name, I would like to add the species info to the sequence name to quickly spot the organism. e.g. my_pet_protein|Escherichia_coli. But then, I would need to change the annotation file seq_name if I can’t use a shorthand…

Thanks
	Steffen
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