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MPI-ClustDB: A fast string matching strategy utilizing parallel computing

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2006

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Gesellschaft für Informatik e.V.

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ClustDB is a tool for the identification of perfect matches in large sets of sequences. It is faster and can handle at least 8 times more data than VMATCH, the most memory efficient exact program currently available. Still ClustDB needs about four hours to compare all Human ESTs. We therefore present a distributed and parallel implementation of ClustDB to reduce the execution time. It uses a message-passing library called MPI and runs on distributed workstation clusters with significant runtime savings. MPI-ClustDB is written in ANSI C and freely available on request from the authors.

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Hamborg, Thomas; Kleffe, Jürgen (2006): MPI-ClustDB: A fast string matching strategy utilizing parallel computing. German Conference on Bioinformatics. Bonn: Gesellschaft für Informatik e.V.. PISSN: 1617-5468. ISBN: 978-3-88579-177-5. pp. 33-39. Regular Research Papers. Tübingen. September 19-22, 2006

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