ParaMEME: A Parallel Implementation and a Web Interface
for a DNA and Protein Motif Discovery Tool
William N. Grundy
Timothy L. Bailey
Charles P. Elkan
CABIOS, 12(4):303-310, 1996 (with corrections).
Abstract
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 Supercomputer Center. ParaMEME scales gracefully to
64 nodes on the Paragon with efficiencies above 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/MEME.
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