Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.

ABSTRACT: Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different wit

SUBMITTER: Wei W 

PROVIDER: S-EPMC3744497 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature