MPBLAST : improved BLAST performance with multiplexed queries.

We have developed a program, MPBLAST, that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed. Throughput was observed to increase in reciprocal proportion to the component sequence length. For sequencing read-sized queries of 500 bp, an order of magnitude speed-up was seen. Free (see http://blast.wustl.edu) [ikorf, gish]@watson.wustl.edu