[Biojava-dev] Blast info

[Andreas Prlic]

Hi Keith,

Blast has historically been a weak point of BioJava, since we did not
have anybody volunteering to work on Blast support. As such our
recommendation is to use the XML output of Blast and then parsing
should be straightforward.

We are using SVN for development. However our public and anonymous SVN
server has been very unreliable last few months and we recommending
getting a checkout via git (there is also a SVN interface to git...).
Alternatively you can get nightly build jars from
http://biojava.org/download/maven/

The download options are described at
http://biojava.org/wiki/CVS_to_SVN_Migration

Andreas

On Wed, Nov 17, 2010 at 9:21 AM, Keith Perry <KPerry at idtdna.com> wrote:
> Does biojava3 plan to include a wrapper for the blast+ local executables like biopython does?  Will it already parse the output of the blast+ executables?  I am starting a project that will use blast+ heavily, and this would save me a ton of time.
>
> Also, are you guys running this out of git or svn?  I thought I saw documentation pointing to svn, but I saw on another thread someone mentioning that you also had it on git.  How can I get to the git repository?
>
> Thanks,
> Keith B. Perry
>
>
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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