Literature DB >> 9021265

Parallel hardware for sequence comparison and alignment.

R Hughey1.   

Abstract

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures is also noted.

Mesh:

Year:  1996        PMID: 9021265     DOI: 10.1093/bioinformatics/12.6.473

Source DB:  PubMed          Journal:  Comput Appl Biosci        ISSN: 0266-7061


  4 in total

1.  ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

Authors:  T Rognes
Journal:  Nucleic Acids Res       Date:  2001-04-01       Impact factor: 16.971

2.  env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area.

Authors:  S Corbet; M C Müller-Trutwin; P Versmisse; S Delarue; A Ayouba; J Lewis; S Brunak; P Martin; F Brun-Vezinet; F Simon; F Barre-Sinoussi; P Mauclere
Journal:  J Virol       Date:  2000-01       Impact factor: 5.103

3.  High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting.

Authors:  István A Bogdán; Jenny Rivers; Robert J Beynon; Daniel Coca
Journal:  Bioinformatics       Date:  2008-05-03       Impact factor: 6.937

4.  160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA).

Authors:  Isaac T S Li; Warren Shum; Kevin Truong
Journal:  BMC Bioinformatics       Date:  2007-06-07       Impact factor: 3.169

  4 in total

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