Bio::Tools::pSW(3pm)					User Contributed Perl Documentation				      Bio::Tools::pSW(3pm)

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

perl v5.14.2							    2012-03-02						      Bio::Tools::pSW(3pm)