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 - 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