Protein-Coding Gene Families in Prokaryote Genome Comparisons

Carhuaricra-Huaman D.; Setubal J.C. · Methods in Molecular Biology (2024) · DOI: 10.1007/978-1-0716-3838-5_2

Resumen

The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many computational tools for the prediction of orthologous groups as well as web-based resources that offer orthology datasets for download and online analysis. This chapter presents a simple and practical guide to the process of orthologous group prediction, using a dataset of 10 prokaryotic proteomes as example. The orthology methods covered are OrthoMCL, COGtriangles, OrthoFinder2, and OMA. The authors compare the number of orthologous groups predicted by these various methods, and present a brief workflow for the functional annotation and reconstruction of phylogenies from inferred single-copy orthologous genes. The chapter also demonstrates how to explore two orthology databases: eggNOG6 and OrthoDB. © The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024.

Instituciones: Universidad Nacional Mayor de San Marcos