Evidence map›Paper›PMID 42411404›Full record

ArticleCurrent protocols2026

Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.

George Bouras, Susanna R Grigson, Lindsay Durr, Bhavya Papudeshi, Vijini Mallawaarachchi, Sarah Vreugde, Robert A Edwards

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Current protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

George BourasSchool of Medicine, College of Health, Adelaide University, Adelaide, Australia.ORCID https://orcid.org/0000-0002-5885-4186
Susanna R GrigsonDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California.
Lindsay DurrSchool of Medicine, College of Health, Adelaide University, Adelaide, Australia.
Bhavya PapudeshiDepartment of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
Vijini MallawaarachchiFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Australia.
Sarah VreugdeSchool of Medicine, College of Health, Adelaide University, Adelaide, Australia.ORCID https://orcid.org/0000-0003-4719-9785
Robert A EdwardsFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Australia.ORCID https://orcid.org/0000-0001-8383-8949

Funding

Australian Research Council
6 · The paper itself

Abstract

Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential of prokaryotic viral metagenomes is extremely challenging. Pharokka, Phold, and Phynteny are complementary open-source prokaryotic viral genome annotation tools that utilize a variety of bioinformatics approaches to maximally annotate viral metagenomes. This article describes a protocol for installing and running these tools on a viral metagenomic dataset, followed by visualization of annotations using our client-side Phold Plot web assembly application. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Prokaryotic viral metagenome annotation with Pharokka Basic Protocol 2: Enhanced prokaryotic viral metagenome protein annotation using protein structures with Phold Basic Protocol 3: Further prokaryotic viral metagenome protein annotation using genome synteny and protein language models with Phynteny Basic Protocol 4: Visualization of prokaryotic viral metagenome annotations with Phold Plot web assembly application.

Indexed as

Computational BiologyGenome, ViralMetagenomeMetagenomicsSoftwareVirusesBacteriophagesMolecular Sequence AnnotationViral ProteinsViral Proteinsbacteriophagegenome annotationmetagenomesprokaryotic virusesprotein functionprotein structure

Identifiers

PMID42411404
PMCPMC13338908

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.