A protocol for generating a high-quality genome-scale metabolic reconstruction.

TitleA protocol for generating a high-quality genome-scale metabolic reconstruction.
Publication TypeJournal Article
Year of Publication2010
AuthorsThiele I, Palsson BØ
JournalNature protocols
Volume5
Issue1
Pagination93-121
PubMed Date2010
ISSN1750-2799
KeywordsBiomass, Computer Simulation, Gene Expression Profiling, Gene Expression Regulation, Genome, Metabolome, Software
Abstract

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

Alternate JournalNat Protoc
PubMed ID20057383

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