Bio::Tools::Run::PiseApplication::clustalw.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::clustalw

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::clustalw
       Bioperl class for:
 
         Clustalw        Multiple Alignments (Des Higgins)
 
         References:
 
                 Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680.
 
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/clustalw.html 
          for available values):
 
 
                 clustalw (String)
 
                 infile (Sequence)
                         Sequences File  (or Alignment File for Bootstrap and Tree actions) (-infile)
                         pipe: seqsfile
                         pipe: readseq_ok_alig
 
                 actions (Excl)
                         Actions
 
                 phylip_alig (Switch)
                         Phylip alignment output format (-output)
 
                 quicktree (Excl)
                         Toggle Slow/Fast pairwise alignments (-quicktree)
 
                 typeseq (Excl)
                         Protein or DNA (-type)
 
                 matrix (Excl)
                         Protein weight matrix (-matrix)
 
                 dnamatrix (Excl)
                         DNA weight matrix (-dnamatrix)
 
                 gapopen (Integer)
                         Gap opening penalty (-gapopen)
 
                 gapext (Float)
                         Gap extension penalty (-gapext)
 
                 endgaps (Switch)
                         End gap separation penalty (-endgaps)
 
                 gapdist (Integer)
                         Gap separation pen. range (-gapdist)
 
                 pgap (Switch)
                         Residue specific penalties (Pascarella gaps) (-nopgap)
 
                 hgap (Switch)
                         Hydrophilic gaps (-nohgap)
 
                 hgapresidues (List)
                         Hydrophilic residues list (-hgapresidues)
 
                 maxdiv (Integer)
                         Delay divergent sequences : % ident. for delay (-maxdiv)
 
                 negative (Switch)
                         Negative values in matrix ? (-negative)
 
                 transweight (Float)
                         Transitions weight (between 0 and 1) (-transweight)
 
                 newtree (OutFile)
                         File for new guide tree (-newtree)
 
                 usetree (InFile)
                         File for old guide tree (-usetree)
 
                 ktuple (Integer)
                         Word size (-ktuple)
 
                 topdiags (Integer)
                         Number of best diagonals (-topdiags)
 
                 window (Integer)
                         Window around best diags (-window)
 
                 pairgap (Float)
                         Gap penalty (-pairgap)
 
                 score (Excl)
                         Percent or absolute score ? (-score)
 
                 pwmatrix (Excl)
                         Protein weight matrix (-pwmatrix)
 
                 pwdnamatrix (Excl)
                         DNA weight matrix (-pwdnamatrix)
 
                 pwgapopen (Float)
                         Gap opening penalty (-pwgapopen)
 
                 pwgapext (Float)
                         Gap extension penalty (-pwgapext)
 
                 kimura (Switch)
                         Use Kimura's correction (multiple substitutions) ? (-kimura)
 
                 tossgaps (Switch)
                         Ignore positions with gaps ? (-tossgaps)
 
                 bootstrap (Integer)
                         Bootstrap a NJ tree (give the number of bootstraps, 0 for none) (-bootstrap)
 
                 bootlabels (Excl)
                         Phylip bootstrap positions (-bootlabels)
 
                 seed (Integer)
                         Seed number for bootstraps (-seed)
 
                 outputtree (Excl)
                         Output tree/distance format (-outputtree)
 
                 outfile (OutFile)
                         Alignment File (-outfile)
                         pipe: readseq_ok_alig
 
                 output (Excl)
                         Output format (-output)
 
                 gde_lower (Switch)
                         Upper case GDE output (-case)
 
                 outorder (Excl)
                         Result order (-outorder)
 
                 seqnos (Switch)
                         Output sequence numbers in the output file (clustalw format) (-seqnos)
 
                 profile1 (InFile)
                         Profile 1 (-profile1)
 
                 profile2 (InFile)
                         Profile 2 (-profile2)
 
                 usetree1 (InFile)
                         File for old guide tree for profile1 (-usetree1)
 
                 usetree2 (InFile)
                         File for old guide tree for profile2 (-usetree2)
 
                 newtree1 (OutFile)
                         File for new guide tree for profile1 (-newtree1)
 
                 newtree2 (OutFile)
                         File for new guide tree for profile2 (-newtree2)
 
                 nosecstr1 (Switch)
                         Use profile 1 secondary structure / penalty mask (-nosecstr1)
 
                 nosecstr2 (Switch)
                         Use profile 2 secondary structure / penalty mask (-nosecstr2)
 
                 helixgap (Integer)
                         Helix gap penalty (-helixgap)
 
                 strandgap (Integer)
                         Strand gap penalty (-strandgap)
 
                 loopgap (Integer)
                         Loop gap penalty (-loopgap)
 
                 terminalgap (Integer)
                         Secondary structure terminal penalty (-terminalgap)
 
                 helixendin (Integer)
                         Helix terminal positions:  number of residues inside helix to be treated as terminal (-helixendin)
 
                 helixendout (Integer)
                         Helix terminal positions: number of residues outside helix to be treated as terminal (-helixendout)
 
                 strandendin (Integer)
                         Strand terminal positions: number of residues inside strand to be treated as terminal (-strandendin)
 
                 strandendout (Integer)
                         Strand terminal positions: number of residues outside strand to be treated as terminal (-strandendout)
 
                 secstrout (Excl)
                         Output in alignment (-secstrout)
 
 

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 (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/clustalw.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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