The In Silico Prediction of Promoters in Bacterial Genomes

Towsey, Michael W., Hogan, James M., Mathews, Sarah A., & Timms, Peter (2007) The In Silico Prediction of Promoters in Bacterial Genomes. In Ng, See-Kiong, Mamitsuka, Hiroshi, & Wong, Limsoon (Eds.) Genome Informatics Workshop 2007, 3rd - 5th December 2007, Singapore.


In silico approaches to the identification of bacterial promoters are hampered by poor conservation of their characteristic binding sites. This suggests that the usual position weight matrix models of bacterial promoters are incomplete. A number of methods have been used to overcome this inadequacy, one of which is to incorporate structural properties of DNA. In this paper we describe an extension of the promoter description to include SIDD (stress induced duplex destabilization), DNA curvature and stacking energy. Although we report the best result to date for a realistic promoter prediction task, surprisingly, DNA structural properties did not contribute significantly to this result. We also demonstrate for the first time, that sigma-54 promoters have a stronger association with SIDD than do other promoter types.

Impact and interest:

6 citations in Scopus
Search Google Scholar™
5 citations in Web of Science®

Citation counts are sourced monthly from Scopus and Web of Science® citation databases.

These databases contain citations from different subsets of available publications and different time periods and thus the citation count from each is usually different. Some works are not in either database and no count is displayed. Scopus includes citations from articles published in 1996 onwards, and Web of Science® generally from 1980 onwards.

Citations counts from the Google Scholar™ indexing service can be viewed at the linked Google Scholar™ search.

Full-text downloads:

256 since deposited on 16 Jul 2008
13 in the past twelve months

Full-text downloads displays the total number of times this work’s files (e.g., a PDF) have been downloaded from QUT ePrints as well as the number of downloads in the previous 365 days. The count includes downloads for all files if a work has more than one.

ID Code: 14073
Item Type: Conference Paper
Refereed: Yes
Additional URLs:
Keywords: bacterial promoters, promoter prediction, duplex destabilization, DNA curvature
ISSN: 0919-9454
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > OTHER BIOLOGICAL SCIENCES (069900) > Biological Sciences not elsewhere classified (069999)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > ARTIFICIAL INTELLIGENCE AND IMAGE PROCESSING (080100) > Pattern Recognition and Data Mining (080109)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2007 (please consult author)
Deposited On: 16 Jul 2008 00:00
Last Modified: 29 Feb 2012 13:36

Export: EndNote | Dublin Core | BibTeX

Repository Staff Only: item control page