Home
Reading
Searching
Subscribe
Sponsors
Statistics
Posting
Contact
Spam
Lists
Links
About
Hosting
Filtering
Features Download
Marketing
Archives
FAQ
Blog
 
Gmane
From: Scott Markel <SMarkel <at> accelrys.com>
Subject: Re: Fwd: RemoteBlast has an upper limit fo 100 returned hits ?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 19th February 2009 01:32:36 UTC (over 8 years ago)
Philip,

I think you want to look at setting the CGI headers for ALIGNMENTS and
DESCRIPTIONS.

The NCBI URL is http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html.

ALIGNMENTS: blastall's -b option
(http://www.ncbi.nlm.nih.gov/BLAST/Doc/node10.html)

DESCRIPTIONS: blastall's -v option
(http://www.ncbi.nlm.nih.gov/BLAST/Doc/node17.html)

HITLIST_SIZE: max of "-b" and "-v" options
(http://www.ncbi.nlm.nih.gov/BLAST/Doc/node30.html)

NCBI sets defaults, but note that Bio::Tools::Run::RemoteBlast
sets its own defaults.

    # Default values go in here for GET
    %RETRIEVALHEADER = (
			'CMD'            => 'Get',
			'ALIGNMENTS'	 => '50',
			'ALIGNMENT_VIEW' => 'Pairwise',
			'DESCRIPTIONS'	 => '100',
			'FORMAT_TYPE'	 => 'Text',
			);

So you're seeing 100 = max(50, 100) hits.  Change the header
values for ALIGNMENTS or DESCRIPTIONS to get a larger number of
hits.  For example,

        $Bio::Tools::Run::RemoteBlast::HEADER{"ALIGNMENTS"} = 200;
        $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{"ALIGNMENTS"} = 200;

In our code I note that I set both HEADER and RETRIEVALHEADER.  I had
problems a few years ago if I only set the RETRIEVALHEADER value.

Hope this helps.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel@accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Vice President, Board of Directors:
    International Society for Computational Biology
Co-chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics


> -----Original Message-----
> From: bioperl-l-bounces@lists.open-bio.org [mailto:bioperl-l-
> bounces@lists.open-bio.org] On Behalf Of Jason Stajich
> Sent: Wednesday, 18 February 2009 12:52 PM
> To: BioPerl list
> Cc: philip.xiang@roche.com
> Subject: [Bioperl-l] Fwd: RemoteBlast has an upper limit fo 100 returned
> hits ?
> 
> Philip - best to ask on the mailing list. fwding it on.
> -jason
> Begin forwarded message:
> 
> > From: "Xiang, Philip" 
> > Date: February 18, 2009 12:37:23 PM PST
> > To: 
> > Subject: RemoteBlast has an upper limit fo 100 returned hits ?
> >
> > Hi Jason,
> >
> >
> >
> > I don't seem to be able to get more than 100 sequences returned with
> > Bio::Tools::Run RemoteBlast.
> >
> > I get 10 hits returned with the following piece of code.
> >
> >  my @params = ( '-prog' => 'blastn',
> >
> >         '-data' => 'nr',
> >
> >         '-expect' => '1e-10',
> >
> >         '-descriptions' => 10,
> >
> >         '-alignments' => 10,
> >
> >         '-readmethod' => 'SearchIO' );
> >
> >  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >
> >  my $r = $factory->submit_blast($input);
> >
> >
> >
> > But I get only 100 hits returned if I change the code to:
> > '-descriptions' => 10000, '-alignments' => 10000, even though the
> > query
> > fetches a lot more hits on NCBI BLAST web interface.
> >
> > What did I do wrong?
> >
> > Thank you in advance for your help!
> >
> >       Phil Xiang
> >
> >       Phone: 925.730.8709
> >
> >
> >
> 
> Jason Stajich
> jason@bioperl.org
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 
CD: 2ms