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

Zusammenfassung
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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  • BibTeX
Hamborg, T. & Kleffe, J., (2006). MPI-ClustDB: A fast string matching strategy utilizing parallel computing. In: Huson, D., Kohlbacher, O., Lupas, A., Nieselt, K. & Zell, A. (Hrsg.), German Conference on Bioinformatics. Bonn: Gesellschaft für Informatik e.V.. (S. 33-39).
@inproceedings{mci/Hamborg2006,
author = {Hamborg, Thomas AND Kleffe, Jürgen},
title = {MPI-ClustDB: A fast string matching strategy utilizing parallel computing},
booktitle = {German Conference on Bioinformatics},
year = {2006},
editor = {Huson, Daniel AND Kohlbacher, Oliver AND Lupas, Andrei AND Nieselt, Kay AND Zell, Andreas} ,
pages = { 33-39 },
publisher = {Gesellschaft für Informatik e.V.},
address = {Bonn}
}
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ISBN: 978-3-88579-177-5
ISSN: 1617-5468
Datum: 2006
Sprache: en (en)
Typ: Text/Conference Paper
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