Dataset Information

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

ABSTRACT: Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.

SUBMITTER: Kalvari I

PROVIDER: S-EPMC7779021 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

Kalvari Ioanna I Nawrocki Eric P EP Ontiveros-Palacios Nancy N Argasinska Joanna J Lamkiewicz Kevin K Marz Manja M Griffiths-Jones Sam S Toffano-Nioche Claire C Gautheret Daniel D Weinberg Zasha Z Rivas Elena E Eddy Sean R SR Finn Robert D RD Bateman Alex A Petrov Anton I AI

Nucleic acids research 20210101 D1

Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam familie ...[more]

PMID: 33211869

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Project description:MotivationViruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases.ResultsHere we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from "conservative" to "eXtremely Conservative" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.AvailabilityThe resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143).Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

Publications

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

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