[Bioperl-l] help on getting annotations
sdavis2 at mail.nih.gov
Wed Mar 16 06:32:56 EST 2005
Try http://source.stanford.edu/cgi-bin/source/sourceSearch if you are
using human, mouse, or rat. If not, then this will be a multi-step
process (there isn't a bioperl function to do this--you will have to
write some code).
On Mar 16, 2005, at 1:49 AM, zhihua li wrote:
> Hi netter!
> I have a series of GenBank Accession Numbers(GB78091, GB90876,...) and
> wanna get as much information as possible about each items. I want to
> know their UniGene ID so that I can tell if there are redundancies
> among them; I want to get their gene descriptions or GO annotations so
> as to group them into functional groups; I want to know their KEGG
> pathway IDs so that I can tell which of them are in the same
> biological pathway, etc.....
> Of course I could submit the seris of accession numbers to each
> different database (GenBank, GO, KEGG...) and get their annotations
> respectively. But as the seris contains a large number of items, I
> think it's better to write a perl script (or use an existing bioperl
> function) to have it done automatically.
> Could anyone give me a hint about how i can write the script or use
> the corresponding bioperl function? I'm new to both perl and bioperl.
> Thanks a lot!
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