Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.

ABSTRACT: Phylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require at least quadratic time as a function of the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profile

SUBMITTER: Moi D 

PROVIDER: S-EPMC7423146 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature