VOGDB—Database of Virus Orthologous Groups

Autor: Lovro Trgovec-Greif, Hans-Jörg Hellinger, Jean Mainguy, Alexander Pfundner, Dmitrij Frishman, Michael Kiening, Nicole Suzanne Webster, Patrick William Laffy, Michael Feichtinger, Thomas Rattei
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: Viruses, Vol 16, Iss 8, p 1191 (2024)
Druh dokumentu: article
ISSN: 1999-4915
DOI: 10.3390/v16081191
Popis: Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up to date as for many cellular genomes. To tackle these problems, we have developed VOGDB, which is a database of virus orthologous groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote similarity. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments, and the third layer uses predicted protein structures to find the most remote similarity. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGD B uses all virus genomes from RefSeq and partially reannotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is the inclusion of both prokaryotic and eukaryotic viruses in the same clustering process, which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at vogdb.org under the CC BY 4.0 license.
Databáze: Directory of Open Access Journals
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje