Toward Reducing Phylostratigraphic Errors and Biases.

ABSTRACT: Phylostratigraphy is a method for estimating gene age, usually applied to large numbers of genes in order to detect nonrandom age-distributions of gene properties that could shed light on mechanisms of gene origination and evolution. However, phylostratigraphy underestimates gene age with a nonnegligible probability. The underestimation is severer for genes with certain properties, creating spurious age distributions of these properties and those correlated with these properties. Here we explore three strategies to reduce phylostratigraphic error/bias. First, we test several alternative homology detection methods (PSIBLAST, HMMER, PHMMER, OMA, and GLAM2Scan) in phylostratigraphy, but fail to find any that noticeably outperforms the commonly used BLASTP. Second, using machine learning, we l

SUBMITTER: Moyers BA 

PROVIDER: S-EPMC6105108 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature