{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T20:29:03Z","timestamp":1791923343641,"version":"4.3.4"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:00:00Z","timestamp":1783555200000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005688","name":"Graduate School","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005688","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses rely on identifying the conserved RNA-dependent RNA polymerase (RdRp) by scanning sequencing datasets with specialized profile Hidden Markov Models (pHMMs). Recently, several new pHMM databases for RdRp detection have been released, each following distinct design principles. However, their relative performance remains unclear, and their accessibility to users without advanced computational expertise is limited. Here, we introduce the RdRp Collaborative Analysis Tool with Collections of pHMMs (RdRpCATCH: https:\/\/github.com\/dimitris-karapliafis\/RdRpCATCH), a platform that consolidates publicly available RdRp pHMM resources into a single, user-friendly framework. RdRpCATCH enables the scanning of (meta)transcriptomic assemblies to discover RNA viruses and provides subsequent taxonomic annotation of detected contigs. A comparative analysis of RdRp pHMM databases reveals that most are highly effective at detecting the known diversity of RNA viruses while minimizing false positives, supporting their joint use within RdRpCATCH. RdRpCATCH is distributed as both a conda package and a web server application (https:\/\/rdrpcatch.bioinformatics.nl), facilitating access for researchers with diverse levels of computational expertise. By integrating multiple pHMM resources, this unified framework addresses fragmentation in the field and reduces technical barriers, enabling comprehensive viral discovery.<\/jats:p>","DOI":"10.1093\/nargab\/lqag076","type":"journal-article","created":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T11:47:05Z","timestamp":1783597625000},"source":"Crossref","is-referenced-by-count":2,"title":["RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3960-6461","authenticated-orcid":false,"given":"Dimitris","family":"Karapliafis","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Wageningen University , Droevendaalsesteeg 1, 6708PB Wageningen ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0894-2484","authenticated-orcid":false,"given":"Uri","family":"Neri","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6209-2233","authenticated-orcid":false,"given":"Ingrida","family":"Olendraite","sequence":"additional","affiliation":[{"name":"Division of Virology, Department of Pathology, Addenbrooke\u2019s Hospital, University of Cambridge , Cambridge, CB2 2QQ ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5602-6600","authenticated-orcid":false,"given":"Justine","family":"Charon","sequence":"additional","affiliation":[{"name":"Fruit Biology and Pathology unit, National Research Institute for Agriculture, Food and Environment, University of Bordeaux , 33140 Villenave d\u2019Ornon ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3650-1221","authenticated-orcid":false,"given":"Shoichi","family":"Sakaguchi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University , Takatsuki 569\u20138686 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6072-1975","authenticated-orcid":false,"given":"Xin","family":"Hou","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, CNRS UMR 2000, Evolutionary Genomics of RNA Viruses unit , F-75015 Paris ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4944-4310","authenticated-orcid":false,"given":"Dick","family":"de\u00a0Ridder","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Wageningen University , Droevendaalsesteeg 1, 6708PB Wageningen ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4361-7636","authenticated-orcid":false,"given":"Mark P","family":"Zwart","sequence":"additional","affiliation":[{"name":"Netherlands Institute of Ecology (NIOO-KNAW) , Droevendaalsesteeg 10, 6708 PB Wageningen ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5237-1899","authenticated-orcid":false,"given":"Anne","family":"Kupczok","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Wageningen University , Droevendaalsesteeg 1, 6708PB Wageningen ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,9]]},"reference":[{"key":"2026070907470337000_B1","doi-asserted-by":"publisher","first-page":"2192","DOI":"10.1073\/pnas.96.5.2192","article-title":"Evolutionary relationships among diverse bacteriophages and prophages: all the world\u2019s a phage","volume":"96","author":"Hendrix","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026070907470337000_B2","doi-asserted-by":"publisher","first-page":"e00052","DOI":"10.1128\/JB.00052-20","article-title":"Are there 1031 virus particles on earth, or more, or fewer?","volume":"202","author":"Mushegian","year":"2020","journal-title":"J Bacteriol"},{"key":"2026070907470337000_B3","doi-asserted-by":"publisher","first-page":"e00053","DOI":"10.1128\/MMBR.00053-21","article-title":"The Baltimore classification of viruses 50 years later: how does it stand in the light of virus evolution?","volume":"85","author":"Koonin","year":"2021","journal-title":"Microbiol Mol Biol Rev"},{"key":"2026070907470337000_B4","doi-asserted-by":"publisher","first-page":"e3000003","DOI":"10.1371\/journal.pbio.3000003","article-title":"Why are RNA virus mutation rates so damn high?","volume":"16","author":"Duffy","year":"2018","journal-title":"PLoS Biol"},{"key":"2026070907470337000_B5","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/B978-0-12-803109-4.00010-6","article-title":"Introduction to RNA viruses","author":"Payne","year":"2017","journal-title":"Viruses"},{"key":"2026070907470337000_B6","doi-asserted-by":"publisher","first-page":"11555","DOI":"10.1128\/JVI.79.18.11555-11558.2005","article-title":"Adaptive value of high mutation rates of RNA viruses: separating causes from consequences","volume":"79","author":"Elena","year":"2005","journal-title":"J Virol"},{"key":"2026070907470337000_B7","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nrmicro2614","article-title":"Why do RNA viruses recombine?","volume":"9","author":"Simon-Loriere","year":"2011","journal-title":"Nat Rev Micro"},{"key":"2026070907470337000_B8","doi-asserted-by":"publisher","first-page":"D776","DOI":"10.1093\/nar\/gkaf1159","article-title":"Virus taxonomy: the database of the International Committee on Taxonomy of Viruses","volume":"54","author":"Black","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B9","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1002\/2211-5463.13626","article-title":"Current trends in RNA virus detection through metatranscriptome sequencing data","volume":"13","author":"Nakagawa","year":"2023","journal-title":"FEBS Open Bio"},{"key":"2026070907470337000_B10","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1038\/nrmicro.2016.177","article-title":"Virus taxonomy in the age of metagenomics","volume":"15","author":"Simmonds","year":"2017","journal-title":"Nat Rev Micro"},{"key":"2026070907470337000_B11","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1111\/1462-2920.16312","article-title":"The RNA virosphere: how big and diverse is it?","volume":"25","author":"Dominguez-Huerta","year":"2023","journal-title":"Environ Microbiol"},{"key":"2026070907470337000_B12","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1111\/1462-2920.16207","article-title":"The global virome: how much diversity and how many independent origins?","volume":"25","author":"Koonin","year":"2023","journal-title":"Environ Microbiol"},{"key":"2026070907470337000_B13","doi-asserted-by":"publisher","first-page":"313","DOI":"10.3390\/v13020313","article-title":"Structure unveils relationships between RNA virus polymerases","volume":"13","author":"M\u00f6nttinen","year":"2021","journal-title":"Viruses"},{"key":"2026070907470337000_B14","doi-asserted-by":"publisher","first-page":"1821","DOI":"10.1093\/nar\/gkg277","article-title":"A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases","volume":"31","author":"Bruenn","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B15","doi-asserted-by":"publisher","first-page":"e105067","DOI":"10.1371\/journal.pone.0105067","article-title":"Profile hidden Markov models for the detection of viruses within metagenomic sequence data","volume":"9","author":"Skewes-Cox","year":"2014","journal-title":"PLoS One"},{"key":"2026070907470337000_B16","doi-asserted-by":"publisher","first-page":"6929","DOI":"10.1016\/j.cell.2024.09.027","article-title":"Using artificial intelligence to document the hidden RNA virosphere","volume":"187","author":"Hou","year":"2024","journal-title":"Cell"},{"key":"2026070907470337000_B17","doi-asserted-by":"publisher","first-page":"btae704","DOI":"10.1093\/bioinformatics\/btae704","article-title":"ViraLM: empowering virus discovery through the genome foundation model","volume":"40","author":"Peng","year":"2024","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B18","doi-asserted-by":"publisher","first-page":"bbaf001","DOI":"10.1093\/bib\/bbaf001","article-title":"VirDetect-AI: a residual and convolutional neural network\u2013based metagenomic tool for eukaryotic viral protein identification","volume":"26","author":"Z\u00e1rate","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026070907470337000_B19","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1006\/jmbi.1998.2221","article-title":"Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods1","volume":"284","author":"Park","year":"1998","journal-title":"J Mol Biol"},{"key":"2026070907470337000_B20","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1038\/s41564-020-0755-4","article-title":"Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome","volume":"5","author":"Wolf","year":"2020","journal-title":"Nat Microbiol"},{"key":"2026070907470337000_B21","doi-asserted-by":"publisher","first-page":"e14055","DOI":"10.7717\/peerj.14055","article-title":"Ribovirus classification by a polymerase barcode sequence","volume":"10","author":"Babaian","year":"2022","journal-title":"PeerJ"},{"key":"2026070907470337000_B22","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/s41586-021-04332-2","article-title":"Petabase-scale sequence alignment catalyses viral discovery","volume":"602","author":"Edgar","year":"2022","journal-title":"Nature"},{"key":"2026070907470337000_B23","doi-asserted-by":"publisher","first-page":"4023","DOI":"10.1016\/j.cell.2022.08.023","article-title":"Expansion of the global RNA virome reveals diverse clades of bacteriophages","volume":"185","author":"Neri","year":"2022","journal-title":"Cell"},{"key":"2026070907470337000_B24","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1126\/science.abm5847","article-title":"Cryptic and abundant marine viruses at the evolutionary origins of Earth\u2019s RNA virome","volume":"376","author":"Zayed","year":"2022","journal-title":"Science"},{"key":"2026070907470337000_B25","doi-asserted-by":"publisher","first-page":"msad060","DOI":"10.1093\/molbev\/msad060","article-title":"Identification of RNA virus\u2013derived RdRp sequences in publicly available transcriptomic data sets","volume":"40","author":"Olendraite","year":"2023","journal-title":"Mol Biol Evol"},{"key":"2026070907470337000_B26","doi-asserted-by":"publisher","first-page":"veac082","DOI":"10.1093\/ve\/veac082","article-title":"RdRp-scan: a bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data","volume":"8","author":"Charon","year":"2022","journal-title":"Virus Evol"},{"key":"2026070907470337000_B27","doi-asserted-by":"publisher","first-page":"1378695","DOI":"10.3389\/fviro.2024.1378695","article-title":"NeoRdRp2 with improved seed data, annotations, and scoring","volume":"4","author":"Sakaguchi","year":"2024","journal-title":"Front Virol"},{"key":"2026070907470337000_B28","doi-asserted-by":"publisher","first-page":"1371958","DOI":"10.3389\/fviro.2024.1371958","article-title":"Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities","volume":"4","author":"Charon","year":"2024","journal-title":"Front Virol"},{"key":"2026070907470337000_B29","doi-asserted-by":"publisher","first-page":"ME22001","DOI":"10.1264\/jsme2.ME22001","article-title":"NeoRdRp: a comprehensive dataset for identifying RNA-dependent RNA polymerases of various RNA viruses from metatranscriptomic data","volume":"37","author":"Sakaguchi","year":"2022","journal-title":"Microb Environ"},{"key":"2026070907470337000_B30","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s40168-018-0422-7","article-title":"The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification","volume":"6","author":"Aiewsakun","year":"2018","journal-title":"Microbiome"},{"key":"2026070907470337000_B31","doi-asserted-by":"publisher","DOI":"10.17863\/CAM.76470","article-title":"Mining diverse and novel RNA viruses in transcriptomic datasets","author":"Olendraite","year":"2021"},{"key":"2026070907470337000_B32","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2026070907470337000_B33","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkae997","article-title":"The Pfam protein families database: embracing AI\/ML","volume":"53","author":"Paysan-Lafosse","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B34","doi-asserted-by":"publisher","first-page":"veae059","DOI":"10.1093\/ve\/veae059","article-title":"Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system","volume":"10","author":"Tian","year":"2024","journal-title":"Virus Evol"},{"key":"2026070907470337000_B35","doi-asserted-by":"publisher","first-page":"veaf074","DOI":"10.1093\/ve\/veaf074","article-title":"Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases","volume":"11","author":"Brown","year":"2025","journal-title":"Virus Evol"},{"key":"2026070907470337000_B36","doi-asserted-by":"publisher","first-page":"D444","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: the protein sequence classification resource in 2025","volume":"53","author":"Blum","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B37","doi-asserted-by":"publisher","first-page":"btad214","DOI":"10.1093\/bioinformatics\/btad214","article-title":"PyHMMER: a Python library binding to HMMER for efficient sequence analysis","volume":"39","author":"Larralde","year":"2023","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B38","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.21105\/joss.01057","article-title":"Altair: interactive statistical visualizations for Python","volume":"3","author":"VanderPlas","year":"2018","journal-title":"J Open Source Softw"},{"key":"2026070907470337000_B39","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"2026070907470337000_B40","doi-asserted-by":"publisher","first-page":"3029","DOI":"10.1093\/bioinformatics\/btab184","article-title":"Fast and sensitive taxonomic assignment to metagenomic contigs","volume":"37","author":"Mirdita","year":"2021","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B41","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026070907470337000_B42","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.1038\/ismej.2013.59","article-title":"Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes","volume":"7","author":"Hingamp","year":"2013","journal-title":"ISME J"},{"key":"2026070907470337000_B43","doi-asserted-by":"publisher","first-page":"msae202","DOI":"10.1093\/molbev\/msae202","article-title":"VirID: beyond virus discovery\u2014an integrated platform for comprehensive RNA virus characterization","volume":"41","author":"Yang","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026070907470337000_B44","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the Universal Protein Knowledgebase in 2025","volume":"53","author":"The UniProt Consortium","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B45","doi-asserted-by":"publisher","first-page":"W547","DOI":"10.1093\/nar\/gkaf394","article-title":"The UniProt website API: facilitating programmatic access to protein knowledge","volume":"53","author":"Ahmad","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070907470337000_B46","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s40793-025-00719-0","article-title":"Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome","volume":"20","author":"Denison","year":"2025","journal-title":"Environmental Microbiome"},{"key":"2026070907470337000_B47","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B48","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2026070907470337000_B49","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B50","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1016\/j.virol.2017.04.010","article-title":"Mitovirus UGA(Trp) codon usage parallels that of host mitochondria","volume":"507","author":"Nibert","year":"2017","journal-title":"Virology"},{"key":"2026070907470337000_B51","doi-asserted-by":"publisher","first-page":"msag088","DOI":"10.1093\/molbev\/msag088","article-title":"Revealing deep evolutionary relationships between RNA viruses using predicted structural models of viral RNA polymerases","volume":"43","author":"M\u00f6nttinen","year":"2026","journal-title":"Mol Biol Evol"},{"key":"2026070907470337000_B52","doi-asserted-by":"publisher","first-page":"veaf074","DOI":"10.1093\/ve\/veaf074","article-title":"Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases","volume":"11","author":"Brown","year":"2025","journal-title":"Virus Evol"},{"key":"2026070907470337000_B53","doi-asserted-by":"publisher","first-page":"vead088","DOI":"10.1093\/ve\/vead088","article-title":"A tale of caution: how endogenous viral elements affect virus discovery in transcriptomic data","volume":"10","author":"Brait","year":"2024","journal-title":"Virus Evol"},{"key":"2026070907470337000_B54","doi-asserted-by":"publisher","first-page":"e14083","DOI":"10.1111\/1755-0998.14083","article-title":"detectEVE: fast, sensitive and precise detection of endogenous viral elements in genomic data","volume":"25","author":"Brait","year":"2025","journal-title":"Mol Ecol Resour"},{"key":"2026070907470337000_B55","doi-asserted-by":"publisher","first-page":"btaf610","DOI":"10.1093\/bioinformatics\/btaf610","article-title":"HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements","volume":"41","author":"Mu\u00f1oz-Baena","year":"2025","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B56","doi-asserted-by":"publisher","first-page":"2226","DOI":"10.1038\/s41467-025-57500-7","article-title":"VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data","volume":"16","author":"Zheng","year":"2025","journal-title":"Nat Commun"},{"key":"2026070907470337000_B57","doi-asserted-by":"publisher","first-page":"btae575","DOI":"10.1093\/bioinformatics\/btae575","article-title":"VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation","volume":"40","author":"Zhu","year":"2024","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B58","doi-asserted-by":"crossref","first-page":"4403","DOI":"10.1007\/s00018-014-1695-z","article-title":"Common and unique features of viral RNA-dependent polymerases","volume":"71","author":"te\u00a0Velthuis","year":"2014","journal-title":"Cell Mol Life Sci"},{"key":"2026070907470337000_B59","doi-asserted-by":"publisher","first-page":"veac038","DOI":"10.1093\/ve\/veac038","article-title":"Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris","volume":"8","author":"Forgia","year":"2022","journal-title":"Virus Evol"},{"key":"2026070907470337000_B60","doi-asserted-by":"publisher","first-page":"btad093","DOI":"10.1093\/bioinformatics\/btad093","article-title":"VirBot: an RNA viral contig detector for metagenomic data","volume":"39","author":"Chen","year":"2023","journal-title":"Bioinformatics"},{"key":"2026070907470337000_B61","doi-asserted-by":"publisher","first-page":"bbae292","DOI":"10.1093\/bib\/bbae292","article-title":"Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review","volume":"25","author":"Yu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2026070907470337000_B62","doi-asserted-by":"publisher","first-page":"bbaf358","DOI":"10.1093\/bib\/bbaf358","article-title":"SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples","volume":"26","author":"Liu","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026070907470337000_B63","doi-asserted-by":"publisher","first-page":"vez061","DOI":"10.1093\/ve\/vez061","article-title":"A new lineage of segmented RNA viruses infecting animals","volume":"6","author":"Obbard","year":"2020","journal-title":"Virus Evol"},{"key":"2026070907470337000_B64","doi-asserted-by":"publisher","first-page":"msae171","DOI":"10.1093\/molbev\/msae171","article-title":"SegVir: reconstruction of complete segmented RNA viral genomes from metatranscriptomes","volume":"41","author":"Tang","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026070907470337000_B65","doi-asserted-by":"publisher","first-page":"veae004","DOI":"10.1093\/ve\/veae004","article-title":"Conserved untranslated regions of multipartite viruses: natural markers of novel viral genomic components and tags of viral evolution","volume":"10","author":"Zhang","year":"2024","journal-title":"Virus Evol"},{"key":"2026070907470337000_B66","doi-asserted-by":"publisher","first-page":"867111","DOI":"10.3389\/fbinf.2022.867111","article-title":"VirHunter: a deep learning-based method for detection of novel RNA viruses in plant sequencing data","volume":"2","author":"Sukhorukov","year":"2022","journal-title":"Front Bioinform"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag076\/68738521\/lqag076.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag076\/68738521\/lqag076.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T11:47:07Z","timestamp":1783597627000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag076\/8729038"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":66,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,6,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag076","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,6,27]]},"article-number":"lqag076"}}