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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Vydané v:BMC bioinformatics Ročník 10; číslo 1; s. 329
Hlavní autori: Van Nguyen, Hoa, Lavenier, Dominique
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 12.10.2009
BioMed Central Ltd
BMC
Predmet:
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
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Popis
Shrnutí: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.
Bibliografia:ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-10-329