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 <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/16/2006 11:31 PM
To: [email protected]
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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