Functional and evolutionary implications of gene orthology
Toni Gabaldón,Eugene V. Koonin +1 more
TLDR
The complexity of the evolution of gene–phenotype relationships is discussed and the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles are assessed.Abstract:
The concepts of orthology and paralogy are fundamental to comparative genomics and are also frequently used for the functional annotation of uncharacterized genes. However, assumptions regarding function have recently been challenged, and the implications of assigning genes as orthologues or paralogues are far from straightforward.read more
Citations
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Journal ArticleDOI
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Jaime Huerta-Cepas,Damian Szklarczyk,Davide Heller,Ana Hernández-Plaza,Sofia K. Forslund,Helen Cook,Daniel R. Mende,Ivica Letunic,Thomas Rattei,Lars Juhl Jensen,Christian von Mering,Peer Bork +11 more
TL;DR: eggNOG as discussed by the authors is a public database of orthology relationships, gene evolutionary histories and functional annotations, with a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes.
Journal ArticleDOI
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas,Kristoffer Forslund,Luis Pedro Coelho,Damian Szklarczyk,Damian Szklarczyk,Lars Juhl Jensen,Christian von Mering,Christian von Mering,Peer Bork +8 more
TL;DR: EggNOG-mapper is developed, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database, and scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark.
Journal ArticleDOI
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Jaime Huerta-Cepas,Damian Szklarczyk,Damian Szklarczyk,Kristoffer Forslund,Helen Cook,Davide Heller,Davide Heller,Mathias C. Walter,Thomas Rattei,Daniel R. Mende,Shinichi Sunagawa,Michael Kuhn,Lars Juhl Jensen,Christian von Mering,Christian von Mering,Peer Bork,Peer Bork +16 more
TL;DR: The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group, and eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees.
Journal ArticleDOI
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
TL;DR: The Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains is presented, demonstrating that the approach exhibits unrivaled speed while maintaining the accuracy of existing methods.
Posted ContentDOI
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Carlos Pérez Cantalapiedra,Ana Hernández-Plaza,Ivica Letunic,Peer Bork,Peer Bork,Jaime Huerta-Cepas +5 more
TL;DR: For example, EggNOG-mapper v2 as mentioned in this paper is a tool for functional annotation based on precomputed orthology assignments, optimized for vast (meta)genomic data sets.
References
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