NAME

Bio::Tools::Run::PiseApplication::phiblast

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::phiblast

      Bioperl class for:

        BLAST2  phi-blast - Pattern-Hit Initiated BLAST (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman)

        References:

                R. Baeza-Yates and G. Gonnet, Communications of the ACM 35(1992), pp. 74-82.

                 S. Wu and U. Manber, Communications of the ACM 35(1992), pp. 83-91.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/phiblast.html 
         for available values):


                phiblast (Excl)
                        Program (-p)

                nb_proc (Integer)

                query (Sequence)
                        Sequence File (-i)
                        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)

                pattern (String)
                        Pattern - Prosite syntax (-k)

                protein_db (Excl)
                        protein db (-d)

                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 (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)

                Descriptions (Integer)
                        How many short descriptions? (-v)

                Alignments (Integer)
                        How many alignments? (-b)

                view_alignments (Excl)
                        Alignment view options  (not with blastx/tblastx) (-m)

                html_output (String)
                        Html output

                seqalign_file (OutFile)
                        SeqAlign file (-J option must be true) (-O)

                believe (Switch)
                        Believe the query defline (-J)

                txtoutput (String)

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

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/phiblast.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $phiblast = Bio::Tools::Run::PiseApplication::phiblast->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::phiblast 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 $phiblast = $factory->program('phiblast');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::phiblast.