Trgovec-Greif, L.; Hellinger, H.-J.; Mainguy, J.; Pfundner, A.; Frishman, D.; Kiening, M.; Webster, N.; Laffy, P.; Feichtinger, M.; Rattei, T. VOGDB - Database of Virus Orthologous Groups. Preprints2024, 2024070238. https://doi.org/10.20944/preprints202407.0238.v1
APA Style
Trgovec-Greif, L., Hellinger, H. J., Mainguy, J., Pfundner, A., Frishman, D., Kiening, M., Webster, N., Laffy, P., Feichtinger, M., & Rattei, T. (2024). VOGDB - Database of Virus Orthologous Groups. Preprints. https://doi.org/10.20944/preprints202407.0238.v1
Chicago/Turabian Style
Trgovec-Greif, L., Michael Feichtinger and Thomas Rattei. 2024 "VOGDB - Database of Virus Orthologous Groups" Preprints. https://doi.org/10.20944/preprints202407.0238.v1
Abstract
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, a database of Virus Orthologous Groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote homology. 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 homology. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGDB uses all virus genomes from RefSeq and partially re-annotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is 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 https://vogdb.org under the CC BY 4.0 license.
Keywords
protein families; orthologous groups; databases; viruses; phages
Subject
Biology and Life Sciences, Virology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
