[Biojava-l] Pairwise Alignment

mark.schreiber at novartis.com mark.schreiber at novartis.com
Tue Apr 25 06:07:59 UTC 2006

Hi -

The appropriate classes for SW and NW pairwise alignment are in the 
org.biojava.bio.alignment package in the CVS (see 

While SW and NW are simple they are not as flexible as the pairwise 
architectures that can be made with HMMs. For a standard pairwise 
alignment I would think that the SW and NW algorithms are fine.

I'm not sure about comparative speed or memory requirements.

- Mark

Joanna Sharman <J.L.Sharman at sms.ed.ac.uk>
Sent by: biojava-l-bounces at lists.open-bio.org
04/19/2006 05:35 PM

        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Pairwise Alignment


I'm new to BioJava so I'm sorry if this question has been asked several
times before.

This is actually sort of in reply to this message from last month:


I'd like to perform a simple pairwise alignment using the
Smith-Waterman class I saw described here:


but I can't find the classes it mentions anywhere on the cvs.  Can you
point me to where they are?

Also, I'm just wondering why the HMM method is preferred to the
Smith-Waterman (or others)?  It seems quite complicated to me, and like
it might require more memory, or am I wrong? :)


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