[Bioperl-l] Remote Blast - Blast Human Genome
Cook, Malcolm
MEC at stowers-institute.org
Thu Jul 20 22:40:55 UTC 2006
Rohan,
'snp/human/human_snp' is the database name you need to use to blast into
human snp database at NCBI
See the following document for the full list (which link was provided to
me via personal correspondace with NCBI helpdesk). Very useful...
Hmm, looming again, there appear now to be two versions:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdblist.html (last
updated 2/7/2006)
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_accessible_blastdbli
st.html (last uypdated 5/29/2006)
Neither are linked to by any other document on the internet (google sez)
including anywhere else at NCBI. Go figure. It should be IMHO since
this info is nowhere else collected.
Of course it may be out of date, but it always has got me through.
Good luck
Malcolm Cook - mec at stowers-institute.org - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO USA
>-----Original Message-----
>From: bioperl-l-bounces at lists.open-bio.org
>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>Sent: Monday, July 17, 2006 4:26 PM
>To: vrramnar at student.cs.uwaterloo.ca; bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] Remote Blast - Blast Human Genome
>
>Okay, I think I may know what's going on a little more now
>with NCBI's BLAST
>interface. Looks like any NCBI BLAST query must use the
>default URL and so
>must set up to proper GET/PUT commands to retrieve everything
>correctly.
>
>Here's the API description for it all:
>
>http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
>
>You could try setting the database to 'snp' or something along
>those lines
>instead of 'nr'; or you could see what the name of the
>database is when you
>use the web form and try setting it to that. According to
>this page, this
>should be possible:
>
>http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpsnpfaq.sectio
>n.SearchdbSNP
>_test._Search_dbSNP_Using_B
>
>The Entrez Query limit was a recommendation for limiting your
>search to a
>set of sequences for human, for instance.
>
>I'll try looking into it a bit more but I'm pretty busy. If you find
>anything out you should probably post it here .
>
>Chris
>
>> Hi Chris,
>>
>> 1. I have tried changing the database to snp or dbSNP but
>neither works.
>> It
>> seems that depending on which type of blast you use(ie, Genome Blast,
>> Blast SNP,
>> normal blast such as blastn, etc...) you see a different listing of
>> databases
>> available for querys. Since you mention that the Blast page I see was
>> generated
>> by Genome, where could I go to see a complete listing of
>databases I can
>> query??
>> Or if you knew off hand which database to search if I only
>wanted dbSNP
>> hits?
>>
>> 2. You also mention, I can limit the search by using Entrez
>terms. Do you
>> mean
>> like:
>> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'abc';
>> where 'abc' is the name of the subject with which you would
>only like to
>> see
>> result of. For example if you put it as 'Homo
>sapiens[Organism]' then only
>> human
>> sequences would be in hit lists.
>> If this is what you mean, what would I change it to, to see
>only hits from
>> dbSNP?
>>
>> Thanks for the ongoing help,
>>
>> Rohan
>>
>> Quoting Chris Fields <cjfields at uiuc.edu>:
>>
>> > I added a method to RemoteBlast in bioperl-live (CVS) if
>you want to
>> play
>> > with changing the URL. I have been thinking about doing
>this for a bit
>> now
>> > but I already see problems.
>> >
>> > Here's the issue: the BLAST page you see is NOT the NCBI BLAST page
>> (note
>> > the differences in the URL) but a user-friendly request
>page, generated
>> on
>> > the fly by Genome, to submit BLAST requests for the
>relevant database.
>> So
>> > changing the URL will not work (even by adding extra
>parameters); you
>> only
>> > get the original HTML web page.
>> >
>> > You could try changing the database or limiting the search using an
>> Entrez
>> > term (which you should be able to include in the request,
>probably by
>> adding
>> > it to the HEADER).
>> >
>> > Chris
>> >
>> > > -----Original Message-----
>> > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> > > bounces at lists.open-bio.org] On Behalf Of
>> vrramnar at student.cs.uwaterloo.ca
>> > > Sent: Thursday, July 13, 2006 5:39 PM
>> > > To: bioperl-l at lists.open-bio.org
>> > > Subject: [Bioperl-l] Remote Blast - Blast Human Genome
>> > >
>> > >
>> > > Hello Again,
>> > >
>> > > I have another question regarding Remote blast but this
>time using
>> Genome
>> > > Blast.
>> > >
>> > > Here is the link:
>> > >
>> > >
>>
>http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606
>> > >
>> > > which again uses the main Blast web site:
>> > >
>> > > http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi
>> > >
>> > > Again I am not sure what to add or what HEADER
>information to change
>> > > within my
>> > > script.
>> > >
>> > > Here is my program, which was the same as the last email:
>> > >
>> > > #!/usr/bin/perl -w
>> > >
>> > > use Bio::Perl;
>> > > use Bio::Tools::Run::RemoteBlast;
>> > >
>> > > my $prog = "blastn";
>> > > my $db = "refseq_genomic";
>> > > my $e_val = 0.01;
>> > >
>> > > my @params = ( '-prog' => $prog,
>> > > '-data' => $db,
>> > > '-expect' => $e_val);
>> > >
>> > > my $factory = new Bio::Tools::Run::RemoteBlast->new(@params);
>> > > $Bio::Tools::Run::RemoteBlast::HEADER{'WWW_BLAST_TYPE'}
>= '????'; <--
>> ---
>> > > what
>> > > do I put here
>> > > #$Bio::Tools::Run::RemoteBlast::HEADER{'?????'} =
>'????'; <--- Do I
>> need
>> > > to add
>> > > any other values to the form inputs
>> > >
>> > > $factory->submit_blast("blast.in");
>> > > $v = 1;
>> > >
>> > > while (my @rids = $factory->each_rid)
>> > > { foreach my $rid ( @rids )
>> > > { my $rc = $factory->retrieve_blast($rid);
>> > > if( !ref($rc) )
>> > > { if( $rc < 0 )
>> > > { $factory->remove_rid($rid);
>> > > }
>> > > print STDERR "." if ( $v > 0 );
>> > > sleep 5;
>> > > }
>> > > else
>> > > { my $result = $rc->next_result();
>> > > my $filename = $result->query_name()."\.out";
>> > > $factory->save_output($filename);
>> > > $factory->remove_rid($rid);
>> > > print "\nQuery Name: ", $result->query_name(), "\n";
>> > > }
>> > > }
>> > > }
>> > >
>> > >
>> > > Both of my questions are very similiar as in I know how
>to use remote
>> > > blast but
>> > > not sure what to change to access the specific blast I want.
>> > >
>> > > Again, any help would be very appreciated!!
>> > >
>> > > Rohan
>> > >
>> > >
>> > >
>> > > ----------------------------------------
>> > > This mail sent through www.mywaterloo.ca
>> > > _______________________________________________
>> > > Bioperl-l mailing list
>> > > Bioperl-l at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>>
>> ----------------------------------------
>> This mail sent through www.mywaterloo.ca
>
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