Analysis of promoter regions for essential genes of bacillus subtilis using PIDA

Catherine Putonti, Yuriy Fofanov

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Identification of transcription binding sites within promoter regions of genomic DNA is imperative for the understanding of the regulatory circuits that direct the expression of genes. Such sites may be identified through biochemical experimentation or computationally. Computational analysis performed on gene promoter regions usually attempts to identify specific patterns and conserved subsequences. The Pattern/ Island Detection Algorithm (PIDA) is designed to identify patterns having multiple islands (common subsequences) in addition to allowing flexibility for both the island size and the distance between islands. In contrast to the general technique, which relies on weight matrices and related information-scoring functions, frequency based criteria is used to estimate statistical significance of such patterns. In 2003, K. Kobayshi et al. estimated the minimal gene set required to sustain bacterial life in Bacillus subtilis to only include 271 of its ≈4100 genes. As an example, PIDA was implemented to run on the set of promoters for these essential genes and the remaining ≈3800 "non-essential" gene promoters. Consequently, several new transcription factor binding site candidates were identified.

Original languageEnglish (US)
Title of host publicationProceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04
EditorsF. Valafar, H. Valafar
Pages276-282
Number of pages7
StatePublished - 2004
Externally publishedYes
EventProceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04 - Las Vegas, NV, United States
Duration: Jun 21 2004Jun 24 2004

Other

OtherProceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04
CountryUnited States
CityLas Vegas, NV
Period6/21/046/24/04

Fingerprint

Bacilli
Genes
Binding sites
Transcription factors
Transcription
Probability density function
DNA
Networks (circuits)

Keywords

  • Algorithm for pattern identification
  • Bacillus subtilis
  • Promoter
  • Transcription factor binding sites

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Putonti, C., & Fofanov, Y. (2004). Analysis of promoter regions for essential genes of bacillus subtilis using PIDA. In F. Valafar, & H. Valafar (Eds.), Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04 (pp. 276-282)

Analysis of promoter regions for essential genes of bacillus subtilis using PIDA. / Putonti, Catherine; Fofanov, Yuriy.

Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. ed. / F. Valafar; H. Valafar. 2004. p. 276-282.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Putonti, C & Fofanov, Y 2004, Analysis of promoter regions for essential genes of bacillus subtilis using PIDA. in F Valafar & H Valafar (eds), Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. pp. 276-282, Proceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04, Las Vegas, NV, United States, 6/21/04.
Putonti C, Fofanov Y. Analysis of promoter regions for essential genes of bacillus subtilis using PIDA. In Valafar F, Valafar H, editors, Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. 2004. p. 276-282
Putonti, Catherine ; Fofanov, Yuriy. / Analysis of promoter regions for essential genes of bacillus subtilis using PIDA. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. editor / F. Valafar ; H. Valafar. 2004. pp. 276-282
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