Phylogenetic profiling: how much input data is enough?

ABSTRACT: Phylogenetic profiling is a well-established approach for predicting gene function based on patterns of gene presence and absence across species. Much of the recent developments have focused on methodological improvements, but relatively little is known about the effect of input data size on the quality of predictions. In this work, we ask: how many genomes and functional annotations need to be considered for phylogenetic profiling to be effective? Phylogenetic profiling generally benefits from an increased amount of input data. However, by decomposing this improvement in predictive accuracy in terms of the contribution of additional genomes and of additional annotations, we observed diminishing returns in adding more than ∼ 100 genomes, whereas increasing the number of annotations remaine

SUBMITTER: Skunca N 

PROVIDER: S-EPMC4332489 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature