PARAMEME - A PARALLEL IMPLEMENTATION AND A WEB INTERFACE FOR A DNA AND PROTEIN MOTIF DISCOVERY TOOL

Many advanced software tools fail to reach a wide audience because the y require specialized hardware, installation expertise, or an abundanc e of CPU cycles. The worldwide web offers a new opportunityfor distrib uting such systems. One such program, MEME, discovers repeated pattern s, called motifs, in sets of DNA or protein sequences. This tool is no w available to biologists over the worldwide web, using an asynchronou s, 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 fr om 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 us e at http://www.sdsc.edu/CompSci/Biomed/ MEME.