An Algorithm for Identification of Regulatory Signals in Unaligned DNA Sequences, Its Testing and Parallel Implementation

Issue title: 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), June 2002, Novosibirsk, Russia

Article type: Research Article

Authors: Danilova, Ludmila V. | Lyubetsky, Vassily A. | Gelfand, Mikhail S.^;

Affiliations: Institute for Information Transmission Problems RAS, Moscow, 101447, Russia | Integrated Genomics-Moscow, Russia | State Scientific Center GosNIIGenetika, Moscow, 113545, Russia

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 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.

Keywords: bioinformatics, regulatory signals, bacterial genomes, orthologous genes, parallel computing, MPI protocol

Journal: In Silico Biology, vol. 3, no. 1-2, pp. 33-47, 2003