Bio::Tools::pSW - pairwise Smith Waterman object use Bio::Tools::pSW; use Bio::AlignIO; my $factory = new Bio::Tools::pSW( '-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 = new Bio::AlignIO(-format => 'msf', -fh => \*STDOUT); $alnout->write_aln($aln); 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. 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: 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!).

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Ewan Birney, birney@sanger.ac.uk or birney@ebi.ac.uk Jason Stajich, jason@bioperl.org 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