ArticleMicrobes and environments2022
NeoRdRp: A Comprehensive Dataset for Identifying RNA-dependent RNA Polymerases of Various RNA Viruses from Metatranscriptomic Data.
Article in Microbes and environments, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
- RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models.NAR genomics and bioinformatics · 2026Article
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- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Long-term maintenance of aMicrobiology spectrum · 2025Article
- "Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes.bioRxiv : the preprint server for biology · 2025Article
- "Paraxenoviridae", a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes.The ISME journal · 2025Article
- Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.Virus evolution · 2025Article
- Towards geospatially-resolved public-health surveillance via wastewater sequencing.Nature communications · 2024Article
- Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil.Journal of virology · 2024Article
- The International Virus Bioinformatics Meeting 2023.Viruses · 2023Article
- Distinct groups of RNA viruses associated with thermoacidophilic bacteria.bioRxiv : the preprint server for biology · 2023Article
- Current trends in RNA virus detection through metatranscriptome sequencing data.FEBS open bio · 2023Review
- The First Identification of a Narnavirus in Bigyra, a Marine Protist.Microbes and environments · 2023Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA viruses are distributed throughout various environments, and most have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on amino acid sequence similarities. A multiple sequence alignment was generated for each cluster, and a hidden Markov model (HMM) profile was created when the number of sequences was greater than three. We further refined 426 HMM profiles by detecting RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. The majority of NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified the majority of RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. NeoRdRp may be repeatedly improved by the addition of new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.
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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 Socratic graph.