Advertisement

Predicting sRNA Genes in the Genome of E. Coli by the Promoter-Search Algorithm PlatProm

  • A. S. Brok-Volchanski
  • I. S. Masulis
  • K. S. Shavkunov
  • V. I. Lukyanov
  • Yu. A. Purtov
  • E. G. Kostyanicina
  • A. A. Deev
  • O. N. OzolineEmail author
Chapter

Abstract

The potentially transcribed regions in the genome of E. coli were searched for on a systematic basis using the novel pattern recognition software PlatProm. PlatProm takes into consideration both the sequence-specific and structure-specific features in the genetic environment of the promoter sites and identifies transcription start points with a very high accuracy. The whole genome scanning by PlatProm along with the expected promoters upstream of the annotated genes identified several hundred of very similar signals in other intergenic regions and in many coding sequences. Most of them are expected as start points for independent RNA transcripts, providing a unique opportunity to reveal genes encoding antisense and/or alternative RNAs. The potential PlatProm as a tool revealing sRNA genes is discussed.

Key words

promoters genome regulatory regions gene expression promoter-search software transcription untranslated RNAs genome annotation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • A. S. Brok-Volchanski
    • 1
  • I. S. Masulis
    • 1
  • K. S. Shavkunov
    • 1
  • V. I. Lukyanov
    • 1
  • Yu. A. Purtov
    • 1
  • E. G. Kostyanicina
    • 1
  • A. A. Deev
    • 2
  • O. N. Ozoline
    • 1
    Email author
  1. 1.Institute of Cell BiophysicsRussian Academy of Sciences, PushchinoMoscow RegionRussia
  2. 2.Institute of Theoretical and Experimental BiophysicsRussian Academy of Sciences, PushchinoMoscow RegionRussia

Personalised recommendations