PHROG: families of prokaryotic virus proteins clustered using remote homology - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles NAR Genomics and Bioinformatics Year : 2022

PHROG: families of prokaryotic virus proteins clustered using remote homology

Abstract

Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.

Domains

Vegetal Biology
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Origin : Publication funded by an institution

Dates and versions

hal-03580568 , version 1 (18-02-2022)

Licence

Attribution - NonCommercial

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Paul Terzian, Eric Olo Ndela, Clovis Galiez, Julien Lossouarn, Rubén Enrique Pérez Bucio, et al.. PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genomics and Bioinformatics, 2022, 3 (3), pp.12 P;. ⟨10.1093/nargab/lqab067⟩. ⟨hal-03580568⟩
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