[Biojava-l] Sequence retrieval

[Jeffrey Rosenfeld]

I am new to this list, so my question might have already been 
discussed, but I cannot find any reference to it in the archive, so 
here goes:
I am trying to find a quick java-only way to retrieve sequences from a 
blast database.  I am writing a program that needs to obtain large 
amounts of sequences from a fairly large database.  I have tried using 
fastacmd, but there is a great slowdown because of teh need to start up 
an external process for each sequence query.  (I cannot execute one 
large fastacmd job because of the large amounts of sequence that I am 
querying. ) I know that biojava has many different formats for storing 
sequences, but I don't want to have to keep two databases of my 
sequences updated.  I am already using the blast database for blast, so 
I don't want another database.
Is there a simple way to implement fastacmd or somethign similar in 
java?  It should not be too hard to do either using JNI or reverse 
engineering the fastacmd code.

Thanks,

Jeff
Jeffrey Rosenfeld
Department of Invertebrate Zoology
American Museum of Natural History

79th Street@ Central Park West
New York, NY 10024
(212)313-7646