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)