Bio::Tools::Run::PiseApplication::blast2(3)

NAME
Bio::Tools::Run::PiseApplication::blast2

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::blast2

      Bioperl class for:

        BLAST2  with gaps (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/blast2.html
         for available values):

                blast_init (String)

                blast2 (Excl)
                        Blast program

                nb_proc (Integer)

                query (Sequence)
                        Sequence File
                        pipe: seqfile

                start_region (Integer)
                        Start of required region in query sequence (-L)

                end_region (Integer)
                        End of required region in query sequence (-L)

                protein_db (Excl)
                        protein db

                nucleotid_db (Excl)
                        nucleotid db

                filter (Switch)
                        Filter query sequence (DUST with blastn, SEG with others) (-F)

                other_filters (Excl)
                        Filtering options (-F must be true)

                lower_case (Switch)
                        Use lower case filtering (-U)

                Expect (Integer)
                        Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e)

                word_size (Integer)
                        Word Size (-W) (zero invokes default behavior)

                dist_hits (Integer)
                        Multiple Hits window size (zero for single hit algorithm) (-A)

                extend_hit (Integer)
                        Threshold for extending hits (-f)

                dropoff_extent (Float)
                        X dropoff for blast extention in bits (0.0 invokes default behavior) (-y)

                keep_hits (Integer)
                        Number of best hits from region to keep (-K)

                gapped_alig (Switch)
                        Perform gapped alignment (not available with tblastx) (-g)

                dropoff (Integer)
                        X dropoff value for gapped alignment (in bits) (-X)

                dropoff_final (Integer)
                        X dropoff value for final alignment (in bits) (-Z)

                mismatch (Integer)
                        Penalty for a nucleotide mismatch (blastn) (-q)

                match (Integer)
                        Reward for a nucleotide match (blastn) (-r)

                matrix (Excl)
                        Matrix (-M)

                open_a_gap (Integer)
                        Cost to open a gap (-G)

                extend_a_gap (Integer)
                        Cost to extend a gap (-E)

                gc_query (Excl)
                        Query Genetic code to use (blastx) (-Q)

                gc_db (Excl)
                        DB Genetic code (for tblast[nx] only) (-D)

                strand (Excl)
                        Query strand to search against database (for blastx and tblastx) (-S)

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

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

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

                show_gi (Switch)
                        Show GI's in deflines (only available for NCBI db such as nrprot) (-I)

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

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

                htmloutput (Switch)
                        Html output

                html4blast_input (String)

                external_links (Switch)
                        Use external web sites for databases entries retrieval links (-e instead of -s)

                one_HSP_per_line (Switch)
                        Draw one HSP per line in image instead of putting all HSP in one line (-l)

                image_query (Switch)
                        Generate images names based on corresponding query (-q)

                restrict_db (InFile)
                        Restrict search of database to GI's in file (-l)

                psi_checkpoint (InFile)
                        PSI-TBLASTN checkpoint file (-R)
                        pipe: psiblast_matrix

                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/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/blast2.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $blast2 = Bio::Tools::Run::PiseApplication::blast2->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::blast2 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 $blast2 = $factory->program('blast2');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::blast2.