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

[George Armhold]

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