Bio::Tools::Run::PiseApplication::psiblast.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::psiblast

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::psiblast
       Bioperl class for:
 
         BLAST2  psiblast - Position Specific Iterative Blast (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman)
 
         References:
 
                 Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,  Nucleic Acids Res. 25:3389-3402.
 
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/psiblast.html 
          for available values):
 
 
                 psiblast (String)
 
                 query (Sequence)
                         Sequence File
                         pipe: seqfile
 
                 start_region (Integer)
                         Start of required region in query (-S)
 
                 end_region (Integer)
                         End of required region in query (-1 indicates end of query) (-H)
 
                 protein_db (Excl)
                         protein db
 
                 filter (Switch)
                         Filter query sequence with SEG (-F)
 
                 Expect (Integer)
                         Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e)
 
                 window (Integer)
                         Multiple hits window size (zero for single hit algorithm) (-A)
 
                 extend_hit (Integer)
                         Threshold for extending hits (-f)
 
                 dropoff_y (Float)
                         Dropoff for blast ungapped extensions in bits (-y)
 
                 gapped_alig (Switch)
                         Perform gapped alignment (-g)
 
                 dropoff (Integer)
                         X dropoff value for gapped alignment (in bits) (-X)
 
                 dropoff_z (Integer)
                         X dropoff value for final gapped alignment (in bits) (-Z)
 
                 matrix (Excl)
                         Matrix (-M)
 
                 open_a_gap (Integer)
                         Cost to open a gap (-G)
 
                 extend_a_gap (Integer)
                         Cost to extend a gap (-E)
 
                 max_passes (Integer)
                         Maximum number of passes to use in  multipass version (-j)
 
                 expect_in_multipass (Float)
                         e-value threshold for inclusion in multipass model (-h)
 
                 pseudocounts (Integer)
                         Constant in pseudocounts for multipass version (-c)
 
                 trigger (Float)
                         Number of bits to trigger gapping (-N)
 
                 Descriptions (Integer)
                         How many short descriptions? (-v)
 
                 Alignments (Integer)
                         How many alignments? (-b)
 
                 view_alignments (Excl)
                         Alignment view options  (not with blastx/tblastx) (-m)
 
                 htmloutput (Switch)
                         HTML output
 
                 seqalign_file (OutFile)
                         SeqAlign file (-J option must be true) (-O)
 
                 believe (Switch)
                         Believe the query defline (-J)
 
                 save_matrix (OutFile)
                         Save PSI-Blast Matrix to file (-C)
                         pipe: psiblast_matrix
 
                 save_txt_matrix (OutFile)
                         Save PSI-BLAST Matrix as text to file (-Q)
 
                 nb_proc (Integer)
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

http://bioweb.pasteur.fr/seqanal/interfaces/psiblast.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $psiblast = Bio::Tools::Run::PiseApplication::psiblast->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::psiblast object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $psiblast = $factory->program('psiblast');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::psiblast.