Microbial genome analysis: the COG approach

MY Galperin, DM Kristensen… - Briefings in …, 2019 - academic.oup.com
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a
popular tool for microbial genome annotation and comparative genomics. Initially created for …

An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice

T Lallemand, M Leduc, C Landès, C Rizzon, E Lerat - Genes, 2020 - mdpi.com
Gene duplication is an important evolutionary mechanism allowing to provide new genetic
material and thus opportunities to acquire new gene functions for an organism, with major …

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic Acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

EV Kriventseva, D Kuznetsov, F Tegenfeldt… - Nucleic acids …, 2019 - academic.oup.com
Abstract OrthoDB (https://www. orthodb. org) provides evolutionary and functional
annotations of orthologs. This update features a major scaling up of the resource coverage …

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

J Huerta-Cepas, D Szklarczyk, K Forslund… - Nucleic acids …, 2016 - academic.oup.com
Abstract eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at
different taxonomic levels, each with integrated and summarized functional annotations …

A scored human protein–protein interaction network to catalyze genomic interpretation

T Li, R Wernersson, RB Hansen, H Horn, J Mercer… - Nature …, 2017 - nature.com
Genome-scale human protein–protein interaction networks are critical to understanding cell
biology and interpreting genomic data, but challenging to produce experimentally. Through …

FlyBase at 25: looking to the future

LS Gramates, SJ Marygold, G Santos… - Nucleic acids …, 2016 - academic.oup.com
Abstract Since 1992, FlyBase (flybase. org) has been an essential online resource for the
Drosophila research community. Concentrating on the most extensively studied species …

OrthoDB in 2020: evolutionary and functional annotations of orthologs

EM Zdobnov, D Kuznetsov, F Tegenfeldt… - Nucleic acids …, 2021 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast
number of available organisms. OrthoDB is leading in the coverage and genomic diversity …

A comprehensive and dated phylogenomic analysis of butterflies

M Espeland, J Breinholt, KR Willmott, AD Warren… - Current Biology, 2018 - cell.com
Summary Butterflies (Papilionoidea), with over 18,000 described species [1], have
captivated naturalists and scientists for centuries. They play a central role in the study of …

OrthoDB v9. 1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

EM Zdobnov, F Tegenfeldt, D Kuznetsov… - Nucleic acids …, 2017 - academic.oup.com
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a
single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing …