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:

         https://redmine.open-bio.org/projects/bioperl/

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