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BMCBI
2010

Predicting phenotypic traits of prokaryotes from protein domain frequencies

8 years 7 months ago
Predicting phenotypic traits of prokaryotes from protein domain frequencies
Background: Establishing the relationship between an organism's genome sequence and its phenotype is a fundamental challenge that remains largely unsolved. Accurately predicting microbial phenotypes solely based on genomic features will allow us to infer relevant phenotypic characteristics when the availability of a genome sequence precedes experimental characterization, a scenario that is favored by the advent of novel highthroughput and single cell sequencing techniques. Results: We present a novel approach to predict the phenotype of prokaryotes directly from their protein domain frequencies. Our discriminative machine learning approach provides high prediction accuracy of relevant phenotypes such as motility, oxygen requirement or spore formation. Moreover, the set of discriminative domains provides biological insight into the underlying phenotype-genotype relationship and enables deriving hypotheses on the possible functions of uncharacterized domains. Conclusions: Fast and ...
Thomas Lingner, Stefanie Mühlhausen, Toni Gab
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke
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