Biblioteca Digital do Instituto Politécnico de Bragança   Instituto Politécnico de Bragança

Biblioteca Digital do IPB >
Escola Superior Agrária >
Ciências Sociais e Exactas >
CSE - Artigos em Revistas Indexados no ISI >

Please use this identifier to cite or link to this item: http://hdl.handle.net/10198/2259

Título: GRASPm: an efficient algorithm for exact pattern-matching in genomic sequences
Autor: Deusdado, Sérgio
Carvalho, Paulo
Palavras-chave: Pattern-matching
Sequence searching and analisys
Motif discovery
Issue Date: 2009
Editora: Inderscience Publishers
Citação: International Journal of Bioinformatics Research and Applications. ISSN 1744-5485. 5:4 (2009) p. 385-401
Resumo: In this paper, we propose Genomic-oriented Rapid Algorithm for String Pattern-match (GRASPm), an algorithm centred on overlapped 2-grams analysis, which introduces a novel filtering heuristic – the compatibility rule – achieving significant efficiency gain. GRASPm’s foundations rely especially on a wide searching window having the central duplet as reference for fast filtering of multiple alignments. Subsequently, superfluous detailed verifications are summarily avoided by filtering the incompatible alignments using the idcd (involving duplet of central duplet) concept combined with pre-processed conditions, allowing fast parallel testing for multiple alignments. Comparative performance analysis, using diverse genomic data, shows that GRASPm is faster than its competitors.
URI: http://hdl.handle.net/10198/2259
ISSN: 1744-5485
Versão do Editor: http://inderscience.metapress.com/link.asp?id=t213508542710676
Appears in Collections:CSE - Artigos em Revistas Indexados no ISI

Files in This Item:

File Description SizeFormat
2009-IJBRA 5404 Deusdado and Carvalho.pdf1,03 MBAdobe PDFView/Open
Statistics
FacebookTwitterDeliciousLinkedInDiggGoogle BookmarksMySpaceOrkut
Formato BibTex mendeley Endnote Logotipo do DeGóis 

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

 


  © Instituto Politécnico de Bragança - Biblioteca Digital - Feedback - Statistics
  Estamos no RCAAP Governo Português separator Ministério da Educação e Ciência   Fundação para a Ciência e a Tecnologia

Financiado por:

POS_C UE