[Biojava-l] Clustalw tutorial

[Simon Brocklehurst]

Guoneng Zhong wrote:

> Hi all,
>
> Is there a tutorial on how to handle ClustalW outputs?
> Thanks,
>

Hi

We're definitely light on documentation for this - I will try to do a
tutorial
on this.    Here's a little explanation... hope it helps.

o The parser simple deals with the *output* from ClustalW.  The
particular
file it deals with is the .aln file that ClustalW produces (see the
ClustalWAlignmentSAXParser JavaDoc for details).

o Thus, ClustalW does *not* have to be installed on the system that
biojava is
installed on.  All you need is access to the .aln file.

o To understand the events produced by any SAX parser in biojava, run
the
biojava application  org.biojava.bio.program.sax.GenericSAXParserTest.
Hint:
remember to specify the full name of the SAXParser i.e.
org.biojava.etc.etc.
The output of this program is an XML document.  If you do this, you'll
see
that the XML produced for multiple alignments is very simple.

o Rather than using the ClustalWAlignmentSAXParser, a better class to
use is
SequenceAlignmentSAXParser.  This is designed to take multiple sequence
alignments from a variety of programs and recognised formats
automatically.
Note - it only recognises ClustalW and Needle (from EMBOSS) right now.


Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com