PLAST: parallel local alignment search tool for database comparison

Background Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is t...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 10; no. 1; p. 329
Main Authors: Van Nguyen, Hoa, Lavenier, Dominique
Format: Journal Article
Language:English
Published: London BioMed Central 12.10.2009
BioMed Central Ltd
BMC
Subjects:
Algorithms
Bioinformatics
Biomedical and Life Sciences
Comparative analysis
Computational biology
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer Science
Databases, Factual
Genomics
Information Storage and Retrieval - methods
Life Sciences
Microarrays
Microcomputers
Nucleotide sequence
Proteins
Quantitative Methods
Software
Receiver Operating Characteristic Score
Cell Broadband Engine
Indexing Part
Seed Extension
Receiver Operating Characteristic Curve
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:Background Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is tending towards more parallelism, leading to the use of chips with two, four and more cores integrated on the same die. The main purpose of this work was to design an effective algorithm to fit with the parallel capabilities of modern microprocessors. Results A parallel algorithm for comparing large genomic banks and targeting middle-range computers has been developed and implemented in PLAST software. The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy. Conclusion A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-10-329