Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs.

ABSTRACT: Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary reconstructions. With a rapidly increasing number of available genomes, the demand for large-scale predictions is also growing. In this contribution, we evaluate and implement major algorithmic improvements that significantly enhance the speed of the analysis without reducing precision. Graph-based detection of (co-)orthologs is typically based on a reciprocal best alignment heuristic that requires an all vs. all comparison of proteins from all species under study. The initial identification of similar proteins is accelerated by introducing an alternative search tool along with a revised search st

SUBMITTER: Klemm P 

PROVIDER: S-EPMC10751348 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature