V-Score-Search

V-Score-Search is an online-search website for the public to search V-scores and VL-scores associated with every protein cluster or family in five widely used public databases including PHROG, VOG, KEGG, Pfam, and eggNOG. V-scores and VL-scores are quantitative metrics to serve as a virus-like signature for differentiating between viral and non-viral protein families and genomes (Fig. 1). We demonstrate specific use cases of V-scores and VL-scores in virus identification, prophage discovery, annotation of host-derived and metabolic proteins on viral genomes, and virus genome binning. V-scores and VL-scores can serve as a metric to define the likelihood of protein families being detected in viruses and enable diverse applications associated with viral genomics, ecology, and evolution. For more detail on V-scores and VL-scores and how they work, please see our paper (https://www.biorxiv.org/content/10.1101/2024.10.24.619987v1).

Fig. 1| Concepts of V-score and VL-score.

a, Workflow of V-score and VL-score generation. Nine representatives of viral taxa are shown here for the diverse viruses used in the study. A scale for VL-scores and VL-scores is displayed by two-sided arrows going from 0 to 10 and <0 to X, respectively, suggesting low scores indicate non-viral and high-scores indicate viral. b, Frequency of virus-associated annotations with V-score ≥ 0.01 and/or VL-score ≥ 0. c, Top five annotations associated with viruses based on VL-scores. d, Distribution of eggNOG VL-score across proteins from prokaryotic chromosomes (n = 7,561,596), plasmids (n = 437,241) and prokaryotic viruses (n = 83,664). The horizontal line that splits the box represents the median, upper and lower sides of the box represent upper and lower quartiles, whiskers are 1.5 times the interquartile ranges and data points beyond whiskers are considered potential outliers. e, Relationship between the fraction of viral proteins used in (d) and eggNOG VL-score.

Getting Started Part 1: Determine the probability that a protein sequence is viral.

Recommended steps before searching:

1. Identify and translate open reading frames in genomes using pyrodigal-gv[1, 2] (github.com/althonos/pyrodigal-gv).
2. Use EggNOG-mapper[3] (parameters: -m mmseqs --evalue 10-5) to annotate the proteins with the eggNOG database. eggNOG: evolutionary gene genealogy Non-supervised Orthologous Groups (http://eggnog6.embl.de/)

Search and assign scores:

1. Search annotations on V-Score-Search (https://anantharamanlab.github.io/V-Score-Search/)
2. Assign VL-score of eggNOG to each protein.

Explanation for scores:

Probability formula for determining whether a protein is viral:

y = 0.21 − 0.09 x + 0.069 x2 − 0.0038 x3 (y: probability; x: eggNOG VL−score)

For example, a 70% probability is indicated by an eggNOG VL-score of 3.97, while a 90% probability corresponds to an eggNOG VL-score of 4.65. If the eggNOG VL-score exceeds 3.97, the probability that a protein is viral surpasses 70%. Similarly, if the eggNOG VL-score exceeds 4.65, the probability that a protein is viral exceeds 90%.

Getting Started Part 2: Determine the probability that a genome sequence is viral

Recommended steps before searching:

1. Identify and translate open reading frames in genomes using pyrodigal-gv[1, 2] (github.com/althonos/pyrodigal-gv).
2. Align translated proteins to Pfam-A[4] HMMs, VOG HMMs, and KEGG[5] KO HMMs using pyhmmer[6, 7] hmmsearch[6] with a maximum e-value of 1e-05.
3. Employ MMseqs2 (parameter: E-value ≤ 10-5) to search the proteins against the PHROG database. Only keep the hit with the highest score. VOG: Virus Orthologous Groups database (https://fileshare.csb.univie.ac.at/vog/) PHROG: Prokaryotic Virus Remote Homologous Groups database (https://phrogs.lmge.uca.fr/) KEGG: Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/) Pfam: a large collection of protein families (http://pfam-legacy.xfam.org/)

Search and assign scores:

1. Search annotations on V-Score-Search (https://anantharamanlab.github.io/V-Score-Search/)
2. Assign V-score and VL-score of KEGG, VOG, Pfam, and PHROG to each protein.
3. Calculate average V-score and VL-score (AV-score and AVL-score) for each genome. The AV-score and AVL-score of KEGG and Pfam are expressed as: AV-score = (Sum of V-score of Proteins with Significant Hits) / (Number of Proteins with Significant Hits); AVL-score = (Sum of VL-score of Proteins with Significant Hits) / (Number of Proteins with Significant Hits).
4. Calculate average V-score and VL-score (AV-score and AVL-score) for each genome. The AV-score and AVL-score of PHROG and VOG are expressed as: AV-score = (Sum of V-score of Proteins with Significant Hits) / (Total Number of Proteins Encoded in A Genome); AVL-score = (Sum of VL-score of Proteins with Significant Hits) / (Total Number of Proteins Encoded in A Genome).

Explanation for scores:

See probability formulae for determining whether a genome is viral in our paper (https://www.biorxiv.org/content/10.1101/2024.10.24.619987v1).

Here we provide a summary table of the probability of genome being viral across different sequence sizes as below:

Table 1 Probability of being viral genomes across different sequence sizes.

Predicted viral genomes were identified based on the following criteria: (1) sequences with at least one AV-score (from VOG, PHROG, KEGG, or Pfam) exceeding the corresponding cutoffs for each fragment size (e.g., a PHROG AV-score > 4.24 or a VOG AV-score > 4.91 for a 2.5 kb scaffold; detailed cutoffs by fragment size are provided in Table 1). For sequences larger than 15 kb, cutoffs for 14−15 kb fragments were used. (2) Sequences meeting criterion (1) were further filtered for completeness >0%, as assessed by CheckV[8] v1.0.13.

Contact

Please contact Karthik Anantharaman ([email protected] or GitHub Issues) with any questions, concerns or comments. Thank you for using V-score-search!

Copyright

V-score-search: Copyright (C) 2024 Kun Zhou, James Kosmopoulos, Etan Dieppa, Peter Badciong, Karthik Anantharaman This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

References

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