Manual Reference Pages - BIO::TOOLS::PSW (3)
Bio::Tools::pSW - pairwise Smith Waterman object
my $factory = Bio::Tools::pSW->new( -matrix => blosum62.bla,
-gap => 12,
-ext => 2,
#use the factory to make some output
# 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);
This module is included with the central Bioperl distribution:
Follow the installation instructions included in the INSTALL file.
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
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.
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!).
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.
email@example.com - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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
Ewan Birney, birney-at-sanger.ac.uk or birney-at-ebi.ac.uk
Jason Stajich, jason-at-bioperl.org
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an underscore _.
Title : pairwise_alignment
Usage : $aln = $factory->pairwise_alignment($seq1,$seq2)
Function: Makes a SimpleAlign object from two sequences
Returns : A SimpleAlign object
Title : align_and_show
Usage : $factory->align_and_show($seq1,$seq2,STDOUT)
Title : matrix()
Usage : $factory->matrix(blosum62.bla);
Function : Reads in comparison matrix based on name
Argument : comparison matrix
Title : gap
Usage : $gap = $factory->gap() #get
: $factory->gap($value) #set
Function : the set get for the gap penalty
Returns : gap value
Arguments : new value
Title : ext
Usage : $ext = $factory->ext() #get
: $factory->ext($value) #set
Function : the set get for the ext penalty
Returns : ext value
Arguments : new value
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