NAME

Bio::Tools::Run::PiseApplication::bl2seq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::bl2seq

      Bioperl class for:

        BL2SEQ  Blast on 2 sequences (NCBI) (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/bl2seq.html 
         for available values):


                bl2seq (Excl)
                        Blast program

                first_sequence (Sequence)
                        First sequence (-i)
                        pipe: seqfile

                first_seq_loc (String)
                        Location on first sequence (-I)

                second_sequence (Sequence)
                        Second sequence (-j)

                second_seq_loc (String)
                        Location on second sequence (-J)

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

                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)

                word_size (Integer)
                        Wordsize (-W) (zero invokes default behavior)

                gapped_alig (Switch)
                        Perform gapped alignment (-g)

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

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

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

                matrix (Excl)
                        Matrix (-M)

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

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

                strand (Excl)
                        Query strands to search against database (-S)

                dbsize (Integer)
                        theor. db size (zero is real size) (-d)

                searchspacesize (Float)
                        Effective length of the search space (use zero for the real size) (-Y)

                outformat (Excl)
                        Output format (-D)

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/bl2seq.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $bl2seq = Bio::Tools::Run::PiseApplication::bl2seq->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::bl2seq 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 $bl2seq = $factory->program('bl2seq');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::bl2seq.