Bio::Tools::Run::PiseApplication::psiblast(3)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR
Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT
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.