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

NAME
Bio::Tools::Run::PiseApplication::fasta

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::fasta

      Bioperl class for:

        FASTA   Sequence database search (version 3) (W. Pearson)

        References:

                Pearson, W. R. (1999) Flexible sequence similarity searching with the FASTA3 program package. Methods in Molecular Biology

                W. R. Pearson and D. J. Lipman (1988), Improved Tools for Biological Sequence Analysis, PNAS 85:2444-2448

                 W. R. Pearson (1998) Empirical statistical estimates for sequence similarity searches. In J. Mol. Biol. 276:71-84

                Pearson, W. R. (1996) Effective protein sequence comparison. In Meth. Enz., R. F. Doolittle, ed. (San Diego: Academic Press) 266:227-258

      Parameters:

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

                fasta (Excl)
                        Fasta program

                query (Sequence)
                        Query sequence File
                        pipe: seqfile

                seqtype (Excl)
                        Is it a DNA or protein sequence (-n)

                protein_db (Excl)
                        Protein Database

                nucleotid_db (Excl)
                        Nucleotid Database

                break_long (Integer)
                        Break long library sequences into blocks (-N)

                ktup (Integer)
                        ktup : sensitivity and speed of the search (protein:2, DNA:6)

                optcut (Integer)
                        OPTCUT : the threshold for optimization. (-c)

                gapinit (Integer)
                        Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

                gapext (Integer)
                        Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

                high_expect (Float)
                        Maximal expectation value threshold for displaying scores and alignments (-E)

                low_expect (Float)
                        Minimal expectation value threshold for displaying scores and alignments (-F)

                nucleotid_match (Integer)
                        Reward for a nucleotid match (-r)

                nucleotid_mismatch (Integer)
                        Penalty for a nucleotid mismatch (-r)

                matrix (Excl)
                        Scoring matrix file (-s)

                X_penalty (Integer)
                        Penalty for a match to 'X' (independently of the PAM matrix) (-x)

                frameshift (Integer)
                        Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

                frameshift_within (Integer)
                        Penalty for frameshift within a codon (fasty/tfasty)(-j)

                threeframe (Switch)
                        Search only the three forward frames (tfasta) (-3)

                invert (Switch)
                        Reverse complement the query sequence (all tfasta) (-i)

                genetic_code (Excl)
                        Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)

                band (Integer)
                        band-width used for optimization (-y)

                swalig (Switch)
                        unlimited Smith-Waterman alignment for DNA (-A)

                noopt (Switch)
                        no limited optimization (-o)

                stat (Excl)
                        Specify statistical calculation. (-z)

                random (Switch)
                        Estimate stat parameters from shuffled copies of each library sequence (-z)

                histogram (Switch)
                        No histogram (-H)

                scores (Integer)
                        number of similarity scores to be shown (-b)

                alns (Integer)
                        number of alignments to be shown (-d)

                html_output (Switch)
                        HTML output (-m)

                markx (Excl)
                        Alternate display of matches and mismatches in alignments

                init1 (Switch)
                        sequences ranked by the z-score based on the init1 score (-1)

                z_score_out (Excl)
                        Show normalize score as (-B)

                showall (Switch)
                        both sequences are shown in their entirety in alignments (fasta only) (-a)

                linlen (Integer)
                        output line length for sequence alignments (max. 200) (-w)

                offsets (String)
                        Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

                info (Switch)
                        Display more information about the library sequence in the alignment (-L)

                statfile (OutFile)
                        Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

                filter (Switch)
                        Lower case filtering (-S)

                outfile (OutFile)
                        pipe: mview_input

                html_outfile (OutFile)

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/fasta.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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