PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology | Zendy

PerChristian Sæbø | Zendy; Søren Andersen | Zendy; J. Myrseth | Zendy; Jon K. Laerdahl | Zendy; Torbjørn Rognes | Zendy

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PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology

Author(s) -

PerChristian Sæbø,

Søren Andersen,

J. Myrseth,

Jon K. Laerdahl,

Torbjørn Rognes

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki423

Subject(s) - smith–waterman algorithm , software , computer cluster , interface (matter) , similarity (geometry) , set (abstract data type) , biology , computer science , sequence alignment , sequence (biology) , identification (biology) , sensitivity (control systems) , bioinformatics , operating system , peptide sequence , artificial intelligence , genetics , programming language , botany , bubble , maximum bubble pressure method , gene , image (mathematics) , electronic engineering , engineering

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith-Waterman and ParAlign. The ParAlign algorithm is similar to Smith-Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at www.paralign.org, where the major public databases can be searched. The software can also be downloaded free of charge for academic use.

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