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An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching
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Saqi, Mansoor, Dobson, Richard J B, Kraben, Preben, Hodgson, D. A. and Wild, David L. (2009) An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching. Journal of Integrative Bioinformatics, Vol.6 (No.1). p. 107. doi:10.2390/biecoll-jib-2009-107 ISSN 1613-4516.
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Official URL: http://dx.doi.org/10.2390/biecoll-jib-2009-107
Abstract
Metabolic models have the potential to impact on genome annotation and on the interpretation of gene expression and other high throughput genome data. The genome of Streptomyces coelicolor genome has been sequenced and some 30% of the open reading frames (ORFs) lack any functional annotation. A recently constructed metabolic network model for S. coelicolor highlights biochemical functions which should exist to make the metabolic model complete and consistent. These include 205 reactions for which no ORF is associated. Here we combine protein functional predictions for the unannotated open reading frames in the genome with \'missing but expected\' functions inferred from the metabolic model. The approach allows function predictions to be evaluated in the context of the biochemical pathway reconstruction, and feed back iteratively into the metabolic model. We describe the approach and discuss a few illustrative examples.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > Q Science (General) | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre |
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Journal or Publication Title: | Journal of Integrative Bioinformatics | ||||
Publisher: | Journal of Integrative Bioinformatics | ||||
ISSN: | 1613-4516 | ||||
Official Date: | 2009 | ||||
Dates: |
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Volume: | Vol.6 | ||||
Number: | No.1 | ||||
Number of Pages: | 1 | ||||
Page Range: | p. 107 | ||||
DOI: | 10.2390/biecoll-jib-2009-107 | ||||
Status: | Not Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | ||||
Grant number: | BB/F003498/1, GR/S29256/01 (BBSRC) |
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