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Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint

Grech, Brian J., Maetschke, Stefan, Mathews, Sarah A., & Timms, Peter (2007) Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint. Research in Microbiology, 158(8-9), pp. 685-693.

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Abstract

Currently, there is a lack of phylogenetic footprinting programmes that can take advantage of multiple whole genome sequences of different species within the same bacterial genus. Therefore, we have developed and tested a position weight matrix-based programme called Footy, that performs genome-wide analysis of bacterial genomes for promoters that phylogenetically footprint. When Footy was used to analyse the non-coding regions upstream of genes from three chlamyidal species for promoters that phylogenetically footprint, it predicted a total of 42 promoters, of which 41 were new. Ten of the 41 new promoters predicted by Footy were biologically assayed in Chlamydia trachomatis by mapping the 5' end of the transcripts for the associated genes. The primer extension assay validated seven of the 10 promoters. When Footy was compared to two other accepted methods for genome-wide prediction of promoters in bacteria (the standard PWM method and MITRA), Footy performed equally as well or better than these programmes. This paper, therefore, shows the value of a bioinformatics programme able to perform genome-wide analysis of bacteria for promoters that phylogenetically footprint.

Impact and interest:

6 citations in Scopus
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6 citations in Web of Science®

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ID Code: 14844
Item Type: Journal Article
Keywords: Bioinformatics, Chlamydia, Phylogenetic footprinting, Promoter
DOI: 10.1016/j.resmic.2007.08.005
ISSN: 0923-2508
Subjects: Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > MEDICAL MICROBIOLOGY (110800) > Medical Bacteriology (110801)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > MICROBIOLOGY (060500) > Bacteriology (060501)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2007 Elsevier
Copyright Statement: Reproduced in accordance with the copyright policy of the publisher.
Deposited On: 12 Sep 2008
Last Modified: 29 Feb 2012 23:40

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