[Bioperl-l] Using bioperl to blast against "Homo sapiens genomic contig sequences," not nr

[Mark Wagner]

I'm trying to accomplish the same thing that

<http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs>

does but with bioperl, Bio::Tools::Run::RemoteBlast in particular.
Setting -data to 'nr' doesn't get the same results.

The "nr" database is "All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS, GSS, or phase 0, 1 or 2 HTGS sequences)." The database I want to
use is "Homo sapiens genomic contig sequences" (that was the database
as described in the result when I used the web form).

Setting -data to "genome" or "genome_hs" (the database names I extracted
from looking at the source to the page above) results in an error.

I looked at all the url parameters in
<http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html> but I didn't see
anything helpful.

Is there a way to blast against this database using bioperl?

-- 
Mark Wagner mark at lanfear.net