Journal article
Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint
Trends in Microbiology, Vol.158(8-9), pp.685-693
2007
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.
Details
- Title
- Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint
- Authors
- B Grech (Author) - Queensland University of TechnologyS Maetchek (Author) - Queensland University of TechnologyS Mathews (Author) - Queensland University of TechnologyPeter Timms (Author) - Queensland University of Technology
- Publication details
- Trends in Microbiology, Vol.158(8-9), pp.685-693
- Publisher
- Elsevier Ltd.
- Date published
- 2007
- DOI
- 10.1016/j.resmic.2007.08.005
- ISSN
- 0966-842X
- Copyright note
- Copyright © 2007. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
- Organisation Unit
- University of the Sunshine Coast, Queensland; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99449226202621
- Output Type
- Journal article
Metrics
108 File views/ downloads
463 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Web Of Science research areas
- Microbiology
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites