Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability

Rangannan, Vetriselvi and Bansal, Manju (2007) Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability. In: Journal of Biosciences, 32 (5). pp. 871-881.

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Abstract

Analysis of various predicted structural properties of promoter regions in prokaryotic as well as eukaryotic genomes had earlier indicated that they have several common features, such as lower stability, higher curvature and less bendability, when compared with their neighboring regions. Based on the difference in stability between neighboring upstream and downstream regions in the vicinity of experimentally determined transcription start sites, a promoter prediction algorithm has been developed to identify prokaryotic promoter sequences in whole genomes. The average free energy (E) over known promoter sequences and the difference (D) between E and the average free energy over the entire genome (G) are used to search for promoters in the genomic sequences. Using these cutoff values to predict promoter regions across entire Escherichia coli genome, we achieved a reliability of 70% when the predicted promoters were cross verifi ed against the 960 transcription start sites (TSSs) listed in the Ecocyc database. Annotation of the whole E. coli genome for promoter region could be carried out with 49% accuracy. The method is quite general and it can be used to annotate the promoter regions of other prokaryotic genomes.

Item Type:	Journal Article
Publication:	Journal of Biosciences
Publisher:	Indian Academy of Sciences
Additional Information:	Copyright of this article belongs to Indian Academy of Sciences.
Keywords:	DNA stability; free energy calculation; promoter; upstream and downstream region
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	31 Jul 2008
Last Modified:	19 Sep 2010 04:48
URI:	http://eprints.iisc.ac.in/id/eprint/15351

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