[Biojava-dev] Java API for Global Alignment

[mark.schreiber at novartis.com]

Hi -

There is not one in BioJava 1.4 although you can do it with an HMM. There 
is an implementation of the NW algorithm in the CVS as well as the SW 
algorithm. These can be downloaded from CVS and will be in the next build 
or snapshot.

- Mark 

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





Russ Kepler <russ at kepler-eng.com>
Sent by: biojava-dev-bounces at lists.open-bio.org
07/07/2006 09:11 PM

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-dev] Java API for Global Alignment


On Tuesday 04 July 2006 04:44 am, Michael Tran wrote:

> Looking for a Java API to do global alignments (something like a 
clustalw
> alignment).

I think most folks have simply implemented a parser for clustalw output to 

generate a FlexibleAlignment when they needed that.  I've got one, and a 
parser for the Paracel CAML output from their genomic scale assembler as 
well.
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