[Bioperl-l] SwissProt/UniProt GN line format changed

[Hilmar Lapp]

I added the capability to parse this and a test to the main trunk.

The parser will write out the GN line(s) in the old format though. Does 
anybody have the requirement at this point that the parser write the 
new format?

The problem with writing the new format is that that would require some 
additions to the object model, because it would require context for the 
individual annotation values ('Name', 'Synonym', 'OrderedLocusName', or 
ORFName). Presently, annotation values do not have context in Bioperl.

	-hilmar

On Wednesday, July 21, 2004, at 05:12  PM, Boris Lenhard wrote:

> I do not know if it has been discussed yet, but the GN (gene name) line
> format recent versions of SwissProt files has been changed:
>
> e.g. old:
>
> GN   ZNF36 OR KOX18 OR ZNF139.
>
> new:
>
> GN   Name=RCHY1; Synonyms=ZNF363, CHIMP, ARNIP;
>
>
> This renders Bio::SeqIO::swiss unable to parse the GN line; as a
> consequence, the resulting annotation object lacks the 'gene_name' key.
>
> Boris
>
> -- 
>
> ==========================================
>  Boris Lenhard, Ph.D.
>  Group Leader, Applied Genome Informatics
>  Center for Genomics and Bioinformatics
>  Karolinska Institutet
>  Berzelius väg 35, B326b
>  171 77 Stockholm, SWEDEN
>  Phone: +46 (0)8 5248 6391
>  FAX: +46 (0)8 32 48 26
>  E-mail: Boris.Lenhard at cgb.ki.se
> ==========================================
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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