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Rfam specifications


Unique identifier OMICS_02787
Name Rfam
Restrictions to use None
Data access Browse
Version 13.0
Content license CC Attribution
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Rfam


  • person_outline Rfam Team
  • person_outline Anton Petrov

Publications for Rfam

Rfam citations


Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

PLoS One
PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] earch the ribosomal RNA sequences, we applied RNAmmer v1.2 Server [] using the option of Bacteria, and then re-confirmed by BLASTn. Introns, tRNAs, and other small RNA were searched by ARAGORN [] and Rfam cmscan v1.1 []. Several important genes and ambiguous sequences were re-confirmed with PCR amplification followed by Sanger sequencing. The annotated plastid genomes were visualized using Organel […]


Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

Sci Rep
PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2

[…] was used to remove low quality bases with Phred score ≤30 and adaptor sequences from 5′ and 3′ end of the read. The adaptor trimmed reads were aligned against nc-RNA sequence databases (GtRNA, piRNA, Rfam& snoRNA)– using Bowtie (version 1.1.2). Remaining reads were used for known miRNA identification. These reads were first aligned to mature and precursor sequence from miRBase 21 miRNA database (H […]


Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] Non-coding RNAs were predicted by aligned A. ipaensis genome assembly to against the Rfam databese (version 12.1) (Nawrocki et al., ). The pre-tRNAs were identified using tRNAscan-SE (Lowe and Eddy, ), pre-rRNAs were predicted using RNAmmer (Lagesen et al., ), pre-snRNAs were annotate […]


Complete Genome Sequence of Multiple Antibiotic Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus)

Genome Announc
PMCID: 5920164
PMID: 29700142
DOI: 10.1128/genomeA.00248-18
call_split See protocol

[…] 4 PacBio reads, with a coverage of 703.34×. Two gapless contigs (2,128,740 bp and 23,538 bp) were obtained after sequence assembly. Gene prediction was conducted using tRNAscan-SE () for tRNA search, Rfam () for rRNA and noncoding RNA search, and Prodigal () for coding sequence (CDS) search. Predicted genes were functionally annotated by homology search against Kyoto Encyclopedia of Genes and Geno […]


Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South South Korea

Genome Announc
PMCID: 5920192
PMID: 29700134
DOI: 10.1128/genomeA.00194-18

[…] peptides and transmembrane helices were predicted using SignalP 4.1 () and TMHMM v2.0 (). rRNA, tRNA, and other miscellaneous features were predicted using RNAmmer v1.2 (), tRNAscan-SE v1.21 (), and Rfam v12.0 ().The draft genome sequence of P. aquatile CR182T is 5,523,543 bp, with a G+C content of 66.3%. The genome is predicted to have 4,544 coding sequences (CDSs), 72 tRNA genes, and 28 rRNA ge […]


Genome centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Biotechnol Biofuels
PMCID: 5911951
PMID: 29713376
DOI: 10.1186/s13068-018-1121-0

[…] ads were trimmed and filtered with the same procedure and parameters as the metagenomic datasets, followed by removal of reads derived from non-coding RNA sequences (including rRNA) as defined in the rfam database [, ] using blastn []. RSEM [] was used to quantify the transcriptional abundances of ORFs predicted from the PGs as well as the unbinned contigs, expressed as transcripts per million (TP […]


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Rfam institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; Systems Biology Graduate Program, Harvard University, Cambridge, MA, USA; National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
Rfam funding source(s)
Supported by the Intramural Research Program of the NIH National Library of Medicine.

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