GenericBioMatch: A novel generic pattern match algorithm for biological sequences

Author

Pan, Youlian ; Famili, A. Fazel

Author_Institution

Inst. for Inf. Technol., Nat. Res. Council of Canada, Ottawa, Ont., Canada

fYear

2003

fDate

11-14 Aug. 2003

Firstpage

562

Lastpage

563

Abstract

GenericBioMatch is a novel algorithm for exact match in biological sequences. It allows the sequence motif pattern to contain one or more wild card letters (eg. Y, R, W in DNA sequences) and one or more gaps of any number of bases. GenericBioMatch is a relatively fast algorithm as compared to probabilistic algorithms, and has very little computational overhead. It is able to perform exact match of protein motifs as well as DNA motifs. This algorithm can serve as a quick validation tool for implementation of other algorithms, and can also serve as a supporting tool for probabilistic algorithms in order to reduce computational overhead. This algorithm has been implemented in the BioMiner software (http://iit-iti.nrc-cnrc.gc.ca/biomine e.trx), a suite of Java tools for integrated data mining in genomics. It has been tested successfully with DNA sequences from human, yeast, and Arabidopsis.

Keywords

DNA; Java; biology computing; cellular biophysics; data mining; genetics; microorganisms; proteins; Arabidopsis; BioMiner software; DNA sequences; GenericBioMatch; Java tools; biological sequence; computational overhead; fast algorithm; genomics; integrated data mining; motif pattern; probabilistic algorithm; wild card letters; yeast; Biology computing; DNA; Data mining; Genomics; Java; Pattern matching; Proteins; Sequences; Software algorithms; Software tools;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Print_ISBN

0-7695-2000-6

Type

conf

DOI

10.1109/CSB.2003.1227408

Filename

1227408