Bio::Tools::Run::PiseApplication::wublast2(3)

NAME
Bio::Tools::Run::PiseApplication::wublast2

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::wublast2

      Bioperl class for:

        WUBLAST2        Wash-U. multi-processors BLAST, with gaps (Gish. W)

        References:

                Gish, Warren (1994-1997).  unpublished.

                Gish, W, and DJ States (1993). Identification of protein coding regions by database similarity search. Nature Genetics 3:266-72.

                Altschul, SF, and W Gish (1996). Local alignment statistics. ed. R. Doolittle. Methods in Enzymology 266:460-80.

                Korf, I, and W Gish (2000). MPBLAST: improved BLAST performance with multiplexed queries. Bioinformatics in press.

                Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990).  Basic local alignment search tool.  J. Mol. Biol. 215:403-10.

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/wublast2.html
         for available values):

                wublast2 (Excl)
                        Blast program

                query (Sequence)
                        Sequence File
                        pipe: seqfile

                nosegs (Switch)
                        Do not segment the query sequence on hyphen (-) characters (-nosegs)

                protein_db (Excl)
                        protein db

                nucleotid_db (Excl)
                        nucleotid db

                compat (Excl)
                        BLAST version

                wordmask (Switch)
                        Use masking instead of filtering (-wordmask)

                filter (Excl)
                        Use filter (-filter/-wordmask)

                maskextra (Switch)
                        Extend masking additional distance into flanking regions (-maskextra)

                lc (Excl)
                        Filter lower-case letters in query

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

                hspmax (Integer)
                        Maximal number of HSPs saved or reported per subject sequence (-hspmax)

                E2 (Float)
                        Expected number of HSPs that will be found when comparing two sequences that each have the same length (E2)

                Cutoff (Float)
                        Cutoff score: threshold for report (S)

                S2 (Float)
                        Cutoff score which defines HSPs (S2)

                W (Integer)
                        Length of words identified in the query sequence (W)

                T (Integer)
                        Neighborhood word score threshold (T)

                nwstart (Integer)
                        Start generating neighborhood words here in query (blastwup/blastwux) (-nwstart)

                nwlen (Integer)
                        Generate neighborhood words over this distance from 'nwstart' in query (blastwup/blastwux) (-nwlen)

                X (Integer)
                        Word hit extension drop-off score (X)

                hitdist (Integer)
                        Maximum word separation distance for 2-hit BLAST algorithm (-hitdist)

                wink (Integer)
                        Generate word hits at every wink-th position (-wink)

                consistency (Switch)
                        Turn off HSP consistency rules for statistics (-consistency)

                hspsepqmax (Integer)
                        Maximal separation allowed between HSPs along query(-hspsepqmax)

                hspsepsmax (Integer)
                        Maximal separation allowed between HSPs along subject (-hspsepsmax)

                span (Excl)
                        Discard HSPs spanned on (-span*)

                nogap (Switch)
                        Do not create gapped alignments (-nogap)

                gapall (Switch)
                        Generate a gapped alignment for every ungapped HSP found (-gapall)

                gapE (Float)
                        Expectation threshold of sets of ungapped HSPs for subsequent use in seeding gapped alignments (-gapE)

                gapE2 (Float)
                        Expectation threshold for saving individual gapped alignments (-gapE2)

                gapS2 (Integer)
                        Cutoff score for saving individual gapped alignments (-gapS2)

                gapW (Integer)
                        Set the window width within which gapped alignments are generated (-gapW)

                gapX (Integer)
                        Set the maximum drop-off score during banded gapped alignment (gapX)

                gapsepqmax (Integer)
                        Maximal permitted distance on the QUERY sequence between two consistent gapped alignments (-gapsepqmax)

                gapsepsmax (Integer)
                        Maximal permitted distance on the subject sequence between two consistent gapped alignments (-gapsepsmax)

                M (Integer)
                        Reward for a nucleotid match (blastwun) (M)

                N (Integer)
                        Penalty for a nucleotid mismatch (blastwun) (N)

                matrix (String)
                        Scoring matrix (PAM or BLOSUM, see help)

                Q (Integer)
                        Open gap penalty (Q)

                R (Integer)
                        Extending a gap penalty (R)

                gcode (Excl)
                        Genetic code to translate the query (blastx,tblastx) (-gcode)

                strand (Excl)
                        which strands (for nucleotid query)

                dbgcode (Excl)
                        Genetic code for database translation (tblastx,tblastn) (-dbgcode)

                dbstrand (Excl)
                        which strands of the database sequences (tblastwun,tblastwux)

                stat (Excl)
                        Use statistics

                wordstats (Switch)
                        Collect word-hit statistics (-stats)

                ctxfactor (Integer)
                        Base statistics on this number of independent contexts or reading frames (-ctxfactor)

                olf (Float)
                        Maximal fractional length of overlap for HSP consistency of two ungapped alignment (-olf)

                golf (Float)
                        Maximal fractional length of overlap for HSP consistency of two gapped alignments (-olf)

                olmax (Integer)
                        Maximal absolute length of overlap for HSP consistency  of two ungapped alignment (default unlimited) (-olmax)

                golmax (Integer)
                        Maximal absolute length of overlap for HSP consistency  of two gapped alignment (default unlimited) (-golmax)

                gapdecayrate (Float)
                        gapdecayrate

                K (Integer)
                        K parameter for ungapped alignment scores (K)

                L (Integer)
                        lambda parameter for ungapped alignment scores (L)

                H (Integer)
                        H parameter for ungapped alignment scores (H)

                gapK (Integer)
                        K parameter for gapped alignment scores (gapK)

                gapL (Integer)
                        lambda parameter for gapped alignment scores (gapL)

                gapH (Integer)
                        H parameter for gapped alignment scores (gapH)

                Histogram (Switch)
                        Histogram (H)

                Descriptions (Integer)
                        How many short descriptions? (V)

                Alignments (Integer)
                        How many alignments? (B)

                sort (Excl)
                        Sort order for reporting database sequences

                postsw (Switch)
                        Perform full Smith-Waterman before output (blastwup only) (-postsw)

                output_file (String)

                output_format (Excl)
                        Output format

                echofilter (Switch)
                        Display filter sequences in output (-echofilter)

                prune (Switch)
                        Do not prune insignificant HSPs from the output lists (-prune)

                topcomboN (Integer)
                        Report this number of consistent (colinear) groups of HSPs (-topcomboN)

                topcomboE (Float)
                        Only show HSP combos within this factor of the best combo (-topcomboE)

                gi (Switch)
                        Display gi identifiers, when available (-gi)

                noseqs (Switch)
                        Do not display sequence alignments (-noseqs)

                cpus (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/wublast2.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $wublast2 = Bio::Tools::Run::PiseApplication::wublast2->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::wublast2 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 $wublast2 = $factory->program('wublast2');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::wublast2.