An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation

Ludmila V. Danilova, Vassily A. Lyubetsky, Mikhail S. Gelfand

Research output: Contribution to journalArticle

Abstract

We describe an algorithm (IRSA) for identification of common regulatory signals in samples of unaligned DNA sequences. The algorithm was tested on randomly generated sequences of fixed length with implanted signal of length 15 with 4 mutations, and on natural upstream regions of bacterial genes regulated by PurR, ArgR and CRP. Then it was applied to upstream regions of orthologous genes from Escherichia coll and related genomes. Some new palindromic binding and direct repeats signals were identified. Finally we present a parallel version suitable for computers supporting the MPI protocol. This implementation is not strictly bounded by the number of available processors. The computation speed linearly depends on the number of processors.

Original languageEnglish (US)
Pages (from-to)33-47
Number of pages15
JournalIn Silico Biology
Volume3
Issue number1-2
StatePublished - Sep 3 2003
Externally publishedYes

Keywords

  • Bacterial genomes
  • Bioinformatics
  • MPI protocol
  • Orthologous genes
  • Parallel computing
  • Regulatory signals

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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