[Biojava-l] Blast xml parsing

[mark.schreiber at novartis.com]

Hi -=

I'm not sure where the percent identity gets sent but you can find out by 
using the example code 
(http://biojava.org/wiki/BioJava:CookBook:Blast:Echo).

It is also a nice code base for making a custom blast parser that is not 
so object heavy.

- 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





Jose Duarte <duarte at molgen.mpg.de>
Sent by: biojava-l-bounces at lists.open-bio.org
06/16/2006 11:31 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Blast xml parsing


I am a newbie to biojava so sorry if questions are too simple!

I am trying to use Biojava's blast xml parsing following the cookbook 
from biojava's web.

So far I managed to parse correctly the xml output from blast getting 
the SeqSimilaritySearchResult object and then the SeqSimilaritySearchHit 
and SeqSimilaritySearchSubHit. From those I could get bit scores, a 
SimpleAlignment object, sequences as SymbolList objects and all kinds of 
things. My question is how to get the percentage identity as well as all 
of those. That must be obvious but I've been looking around and couldn't 
find how.

Any pointers appreciated

Thanks

Jose


----
Jose M. Duarte
Max Planck Institute for Molecular Genetics
Ihnestr. 63-73
14195 Berlin
Germany

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