PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
Author
Fuentes, Diego
Molina, Manuel
Chorostecki, Uciel
Capella-Gutiérrez, Salvador
Marcet-Houben, Marina
Gabaldón, Toni
Publication date
2022ISSN
0305-1048
Abstract
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
5 - Natural Sciences
Keywords
Ciència i matemàtiques
Ciencias y Matemáticas
Science and Mathematics
Pages
6
Publisher
Oxford University Press
Collection
50; D1
Is part of
Nucleic Acids Research
Citation
Fuentes, Diego; Molina, Manuel; Chorostecki, Uciel [et al.]. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Research, 2022, 50(D1), D1062-1068. Disponible en: <https://academic.oup.com/nar/article/50/D1/D1062/6414570>. Fecha de acceso: 7 feb. 2024. DOI: 10.1093/nar/gkab966
This item appears in the following Collection(s)
- Ciències Bàsiques [65]
Rights
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.