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

[Wiepert, Mathieu]

Hi,

I am not sure if this is right, but I think that you answered your own question without realizing it.  The base URL for the RemoteBlast program is 

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi.  There are separate blast pages for the human genome, at

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

I don't think you can use the databases from the human genome page (second link) with the first, which is what you discovered (if anyone can verify that it would be great)

Following this first link brings you to the basic blast page, (for me it was a protein-protein page).  I flipped to the nucleotide page (link at the top of the page, sure you have seen it), and looked at available db's.  The closest I can come so far is the chromosome db, with an entrez limit of Homo Sapiens (link at bottom, I am sure it will be mangled by delivery)

What I don't know, is what is in the chromosome, except for what it says 
"chromosome Searches Complete Genomes, Complete Chromosome, or contigs form the NCBI Reference Sequence project" 

I am not sure if that is what you want, or if you can use entrez limits to further filter that to just contigs, etc.  You can at least limit it to homo-sapiens with an entrez limit.  If qblast can do it, then RemoteBlast can, just a question of really understanding the main blast page and all it's parameters, and I don't really know that information very well.


blastn on chromosome db, with Homo-Sapiens limit.

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=Semiauto&CLIENT=web&DATABASE=chromosome&DESCRIPTIONS=100&ENTREZ_QUERY=Homo+sapiens+[ORGN]&EXPECT=10&FILTER=L&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_ENTREZ_QUERY=(none)&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&LAYOUT=TwoWindows&NCBI_GI=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS=Yes&SET_DEFAULTS.x=26&SET_DEFAULTS.y=6&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&WORD_SIZE=11&END_OF_HTTPGET=Yes

HTH,

-Mat



-----Original Message-----
From: Mark Wagner [mailto:mark at lanfear.net]
Sent: Tuesday, March 11, 2003 1:46 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Using bioperl to blast against "Homo sapiens
genomiccontig sequences," not nr


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
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