Bio::Tools::pSW.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::pSW - pairwise Smith Waterman object

SYNOPSIS

     use Bio::Tools::pSW;
     use Bio::AlignIO;
     my $factory = Bio::Tools::pSW->new( '-matrix' => 'blosum62.bla',
                                        '-gap' => 12,
                                        '-ext' => 2,
                                        );
 
     #use the factory to make some output
 
     $factory->align_and_show($seq1,$seq2,STDOUT);
 
     # make a Bio::SimpleAlign and do something with it
 
     my $aln = $factory->pairwise_alignment($seq1,$seq2);
     my $alnout = Bio::AlignIO->new(-format => 'msf',
                                   -fh     => \*STDOUT);
 
     $alnout->write_aln($aln);
 
 

INSTALLATION

This module is included with the central Bioperl distribution:
    http://bio.perl.org/Core/Latest
    ftp://bio.perl.org/pub/DIST
 
 

Follow the installation instructions included in the INSTALL file.

DESCRIPTION

pSW is an Alignment Factory for protein sequences. It builds pairwise alignments using the Smith-Waterman algorithm. The alignment algorithm is implemented in C and added in using an XS extension. The XS extension basically comes from the Wise2 package, but has been slimmed down to only be the alignment part of that (this is a good thing!). The XS extension comes from the bioperl-ext package which is distributed along with bioperl. Warning: This package will not work if you have not compiled the bioperl-ext package.

The mixture of C and Perl is ideal for this sort of problem. Here are some plus points for this strategy:

Speed and Memory
The algorithm is actually implemented in C, which means it is faster than a pure perl implementation (I have never done one, so I have no idea how faster) and will use considerably less memory, as it efficiently assigns memory for the calculation.
Algorithm efficiency
The algorithm was written using Dynamite, and so contains an automatic switch to the linear space divide-and-conquer method. This means you could effectively align very large sequences without killing your machine (it could take a while though!).

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 one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Ewan Birney, birney-at-sanger.ac.uk or birney-at-ebi.ac.uk

CONTRIBUTORS

Jason Stajich, jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore ``_''.

pairwise_alignment

  Title   : pairwise_alignment
  Usage   : $aln = $factory->pairwise_alignment($seq1,$seq2)
  Function: Makes a SimpleAlign object from two sequences
  Returns : A SimpleAlign object
  Args    :
 
 

align_and_show

  Title   : align_and_show
  Usage   : $factory->align_and_show($seq1,$seq2,STDOUT)
 
 

matrix

  Title     : matrix()
  Usage     : $factory->matrix('blosum62.bla');
  Function  : Reads in comparison matrix based on name
            :
  Returns   : 
  Argument  : comparison matrix
 
 

gap

  Title     : gap
  Usage     : $gap = $factory->gap() #get
            : $factory->gap($value) #set
  Function  : the set get for the gap penalty
  Example   :
  Returns   : gap value 
  Arguments : new value
 
 

ext

  Title     : ext
  Usage     : $ext = $factory->ext() #get
            : $factory->ext($value) #set
  Function  : the set get for the ext penalty
  Example   :
  Returns   : ext value 
  Arguments : new value