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  An Algorithm for Identification of Regulatory Signals in Unaligned DNA Sequences, Its Testing and Parallel Implementation
 
 
Title: An Algorithm for Identification of Regulatory Signals in Unaligned DNA Sequences, Its Testing and Parallel Implementation
Author: Ludmila V. Danilova
Vassily A. Lyubetsky
Mikhail S. Gelfand
Appeared in: In silico biology
Paging: Volume 3 (2003) nr. 1-2 pages 33-47
Year: 2003-09-02
Contents: 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 coli 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.
Publisher: IOS Press
Source file: Elektronische Wetenschappelijke Tijdschriften
 
 

                             Details for article 2 of 19 found articles
 
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