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.

Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

“…Genes in all genomes included in the initial ViPTree analysis (Table 2) were predicted and annotated using Prokka 1.14.6 (34) using the PHROG (41) dataset. Data were imported into R using Biostrings v2.58.0 (42) and predicted protein names searched for ‘HNH | homing’ to identify HENs encoded with the phage genomes.…”

Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

“…These 11,745 proteins were clustered into groups of orthologous proteins (OG) using a two-step procedure involving remote homology detection (Table S4). Ogs were then functionally annotated using HMM comparisons to the PHROG database [29]. Considering only the 204 transposable (pro)phages, their 11,500 proteins are organized into 480 Ogs with at least two proteins and 392 singletons.…”

“…Finally, using the same tools, multiple alignments and HMM profiles were computed for all OGs. The OGs HMM profiles were compared to the HMM profiles of the PHROG database [29] (annotation release v2), which contains well annotated protein clusters of prokaryotic viruses. This provided a probable functional annotation for OGs similar with at least one PHROG profile.…”

Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy Against the Phytopathogen<em> Ralstonia solanacearum</em>

“…The size of these DTRs was 281 bp for vRsoP-WF2 and vRsoP-WR2, and 280 bp for vRsoP-WM2. [61]. The genomic map was generated with the genome comparison visualiser EasyFig 2.2.5 [62].…”

“…Genes grouped in different functional categories are shown in different colours according to the legend below the map. The categories of the phage proteins of RsoP1EGY and DU_RP_I were extracted from PHROG database[61]. The genomic map was generated with the genome comparison visualiser EasyFig 2.2.5[62].…”