- Article -
| In Silico Biology 3, 0004 (2003); ©2003, Bioinformation Systems e.V. |
An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation
Ludmila V. Danilova1,*, Vassily A. Lyubetsky1 and Mikhail S. Gelfand2,3
1 Institute for Information Transmission Problems RAS, Moscow, 101447, Russia
2 Integrated Genomics-Moscow, Russia
3 State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
Email: dlv2k@mail.ru
* corresponding author
Edited by T. Werner; received September 30, 2002; revised and accepted April 04, 2003; published April 14, 2003
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.
Key words: bioinformatics, regulatory signals, bacterial genomes, orthologous genes, parallel computing, MPI protocol