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