原核生物基因组比较中的蛋白质编码基因家族。

Protein-Coding Gene Families in Prokaryote Genome Comparisons.

机构信息

Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil.

Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru.

出版信息

Methods Mol Biol. 2024;2802:33-55. doi: 10.1007/978-1-0716-3838-5_2.

DOI:10.1007/978-1-0716-3838-5_2

PMID:38819555

Abstract

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.

摘要

同源基因的鉴定对于比较基因组学、系统发育分析和功能注释非常重要。有许多用于预测同源基因簇的计算工具，以及提供同源数据集下载和在线分析的基于网络的资源。本章以 10 个原核蛋白质组数据集为例，提供了一个简单实用的同源基因簇预测过程指南。所涵盖的同源基因方法包括 OrthoMCL、COGtriangles、OrthoFinder2 和 OMA。作者比较了这些不同方法预测的同源基因簇数量，并提出了一个从推断的单拷贝同源基因重建系统发育和功能注释的简要工作流程。本章还演示了如何探索两个同源基因数据库：eggNOG6 和 OrthoDB。