[Bioperl-l] Getting gene symbol and gene descriptions

John O. Woods bamboowarrior at gmail.com
Mon Oct 27 20:08:39 EDT 2008


Hi folks,

I have lists of protein-coding genes in fruit fly (by FlyBase id), and in
arabidopsis thaliana (by TAIR locus ID: AT...). I need to get the gene
symbol name and gene description for each of these.

I tried using GenPept::get_Stream_by_id, but I can't figure out how to
extract the symbol or description that way.

I've also tried BioMart, but that doesn't seem to have data for Arabidopsis
(and it's timing out for fruit fly for some reason).

There's also a flat file on TAIR's website, but it looks to be out of date.
I'd much prefer to get the symbols that are considered "primary" in GenPept.


I was also wondering: I know FlyBase allows anonymous access to its Chado
DB. Is this possible with TAIR? They seem to ignore my emails, sadly--or
perhaps I'm sending them to the wrong place.

Cheers,
John Woods
UT Austin


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