ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool
Department of Computer Science and Engineering, University of California at San Diego La Jolla, CA 92093-0114
1San Diego Supercomputer Center P O Box 85608, UPS, Fed Ex: 10100 Hopkins Drive, San Diego, CA 92186-9784, USA E-mail: bgrundy{at}cs.ucsd.edu, tbailey{at}sdsc.edu, elkan{at}cs.ucsd.edu
Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://www. sdsc . edu/CompSci/Biomed/ MEME.
Received on April 6, 1996; accepted on June 10, 1996
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