Structure-specific modules as indicators of promoter DNA in bacterial genomes

S. S. Kiselev ; O. N. Ozoline

Matematičeskaâ biologiâ i bioinformatika, Tome 6 (2011) no. 1, pp. 39-52.

Résumé

A unified version of promoter-search software, exploiting evolutionary conservation in the structural organization of bacterial transcription machinery is suggested (PlatPromU). In contrast with the initial algorithm PlatProm, optimized for recognition of $\sigma^\mathrm D$-dependent promoters in the genome of Escherichia coli (E.coli), modified version does not use weight matrices, reflecting the occurrence frequency of consensus base pairs within $-10$ and $-35$ elements. Its predicting potentiality was assessed by the ability to recognize the known promoters of Corynebacterium glutamicum (C.glutamicum) – an evolutionarily distant from E.coli microorganism. “Sensitivity” of PlatPromU appeared to be comparable with that of specialized program (PlatPromC), adapted for recognition of C.glutamicum regulatory sites, and higher than predicting potentiality of initial algorithm PlatProm. The unified program, modeling only structural and conformational features of promoter DNA, may, therefore, be recommended as a tool for preliminary mapping of regulatory sites in genomes with unknown context of specific elements.

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