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
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