Ewan Birney


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


    # 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);



This module is included with the central Bioperl distribution:


Follow the installation instructions included in the README file.


pSW is an Alignment Factory. 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 conquor method. This means you could effectively align very large sequences without killing your machine (it could take a while though!).


warning - this module is under active development. Eventually it should contain the ability to make alignment objects such as Bio::SimpleAlign or Bio::UnivAlign

(Which has been done as of bioperl 0.7 series)


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:



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 "_".


 Title   : pairwise_alignment
 Usage   : $aln = $factory->pairwise_alignment($seq1,$seq2)
 Function: Makes a SimpleAlign object from two sequences
 Returns : A SimpleAlign object
 Args    :


 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
 Returns   : 
 Argument  : comparison matrix


 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


 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