Gesellschaft fr Informatik e.V.

Lecture Notes in Informatics


German Conference on Bioinformatics P-83, 33-39 (2006).

Gesellschaft für Informatik, Bonn
2006


Copyright © Gesellschaft für Informatik, Bonn

Contents

MPI-ClustDB: A fast String Matching Strategy Utilizing Parallel Computing

Thomas Hamborg and Jürgen Kleffe

Abstract


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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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-177-5


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