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Briefings in Bioinformatics Advance Access originally published online on November 17, 2007
Briefings in Bioinformatics 2008 9(1):34-45; doi:10.1093/bib/bbm051
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes

Matteo Brilli, Renato Fani and Pietro Liò

Corresponding author. Matteo Brilli, Department of Animal Biology and Genetics, University of Florence, Via Romana 17/19, 50125 Firenze, Italy. Tel: +39052288244; Fax: +390552288250; E-mail: matteo.brilli{at}dbag.unifi.it

The study of metabolic pathways is becoming increasingly important to exploit an integrated, systems-level approach for optimizing a desired cellular property or phenotype. In this context, the integration of genomics data with genetic, metabolic and regulatory models is essential because the systematic design of artificial, biological systems requires the identification of robust building blocks like gene promoters, metabolic pathways or genetic circuits taken from natural organisms, and manipulated to develop ad hoc features. Computational tools allowing precise descriptions of natural pathways might thus allow improving the performance of artificial routes. In this review, we introduce the most recent bioinformatics tools enabling detailed characterizations of metabolic pathways in bacteria from different perspectives.

Keywords: metabolic engineering, pathway, bioinformatics

Submitted: July 26, 2007. Received (in revised form): October 10, 2007.


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