[Biojava-l] introduction, and some BLAST/Genscan code

[Matthew Pocock]

Thanks George,

This looks like realy cool code. It is the part we are missing from the
process. CAT checked in blast parsing code (very cool) and Gerald Loeffler
checked in a set of interfaces for requesting and representing blast hits.
A standard object that actualy performs the blast search would be great.

If you are interested in contributing and maintaining this code and/or
becoming a BioJava developer, I can sort you out with a CVS account. In
the mean time, I will read through the rest of your docs. You may like to
look at the documentation for the packages:

org.biojava.bio.search
org.biojava.bio.program
org.biojava.bio.program.sax
org.biojava.bio.program.xml

We are betwen releases at the moment (hopefuly we should be able to get a
1.1 out the door in the not-to-distant future...), so none of the APIs are
above discussion.

Thanks for the message. All the best,

Matthew

George Armhold wrote:

> Hello,
>
> I just subscribed to the biojava list and would like to say hello to
> everyone, as well as offer up some code.  Browsing through the list
> archives I found a message from Vijay Narayanasamy who was looking for
> some code to talk to the BLAST server at NCBI.  It so happens that I
> just completed such a class, and I'm happy to share it with anyone
> that may find it useful. Here's a (simplified) example:
>
>        String mySequence = createSequence();
>        BlastConnection blast = new BlastConnection();
>        blast.setQuerySequence(mySequence);
>        blast.setProgram(BlastConnection.BLASTN);
>        blast.setDatabase(BlastConnection.DBEST);
>        blast.setExpect(10f);
>        String requestID = blast.submit();
>
>        // wait some amount of time for server to process
>
>        String results = blast.getResults(requestID);
>        if (results.equals(BlastConnection.IN_PROGRESS))
>           System.out.println("request ID " + requestID + " is still in
> progress.
> ");
>        else
>           System.out.println(results);
>
> I also have some code for talking to a Genscan server.  The code has
> been in use at our site for a few weeks, but has not seen extensive
> testing yet.  Source, binaries and documentation are available at
> http://bigbio.rutgers.edu/~armhold/bioinf.
>
> --
> George Armhold
> Rutgers University
> Bioinformatics Initiative
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