[Biojava-dev] Blast info

[Andreas Prlic]

Hi Keith,

There is a Cookbook page:

http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser

Andreas

On Fri, Nov 19, 2010 at 6:15 AM, Keith Perry <KPerry at idtdna.com> wrote:
> Andreas,
> Is there some documentation of what the biojava blast code already does, and what you would like it to do?  Since biopython already has this functionality, it might be easy to compare if I know what biojava currently has for blast...if there is some documentation laying around...otherwise I will dig through the code.  Also, while I would like to use biopython (since the functionality is already there), for the size of the project I am working on, it makes more sense to use Java.
>
> I might be able to convince my boss to let me write the biojava modules (or at least some of them) because I need this functionality anyway.
>
> -----Original Message-----
> From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
> Sent: Thursday, November 18, 2010 11:11 AM
> To: Keith Perry
> Cc: biojava-dev at lists.open-bio.org
> Subject: Re: [Biojava-dev] Blast info
>
> 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
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>



-- 
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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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