On the parallelisation of bioinformatics applications

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structure...

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Bibliographic Details
Published in:Briefings in bioinformatics 2001-05, Vol.2 (2), p.181-194
Main Author: Trelles, O
Format: Article
Language:English
Subjects:
Algorithms
Animals
Bioinformatics
Computational Biology
Computer Systems
Databases, Factual
Humans
Information technology
Software
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Summary:This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/2.2.181