Predicting phenotypic traits of prokaryotes from protein domain frequencies.

ABSTRACT:

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 high-throughput 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 dis

SUBMITTER: Lingner T 

PROVIDER: S-EPMC2955703 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature