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

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 journal › Article › peer-review

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 language	English (US)
Pages (from-to)	33-47
Number of pages	15
Journal	In Silico Biology
Volume	3
Issue number	1-2
State	Published - Sep 3 2003
Externally published	Yes

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

Cite this

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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.",

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PY - 2003/9/3

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N2 - 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.

AB - 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.

KW - Bacterial genomes

KW - Bioinformatics

KW - MPI protocol

KW - Orthologous genes

KW - Parallel computing

KW - Regulatory signals

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

Abstract

Keywords

ASJC Scopus subject areas

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