2012
DOI: 10.1093/nar/gks1005
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Rfam 11.0: 10 years of RNA families

Abstract: The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based a… Show more

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Cited by 745 publications
(648 citation statements)
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“…Jalview was used to calculate the number and percentage of ‐1n = C. The quality of the alignment was also checked by comparison with a recent alignment of box C/D sequences deposited on Rfam 62, 63.…”
Section: Methodsmentioning
confidence: 99%
“…Jalview was used to calculate the number and percentage of ‐1n = C. The quality of the alignment was also checked by comparison with a recent alignment of box C/D sequences deposited on Rfam 62, 63.…”
Section: Methodsmentioning
confidence: 99%
“…All gene models were automatically screened to highlight possible erroneous structures (for example, in-frame stop codons, deviating splice junctions) and manually curated. Transfer-RNA gene models were predicted by tRNAscan-SE (v. 1.31) 57 and their structures were verified with Infernal (v. 1.1rc1, rfam11 covariant model database) 58 . For each gene, UTRs were assigned by identifying a set of ESTs and RNA-seq assemblies that uniquely overlapped with it.…”
Section: )mentioning
confidence: 99%
“…We identified a high proportion of antisense and coding messenger RNA sequences, as well as abundant lincRNA sequences (Figure 8(a)), but a very low relative abundance of miRNAs (0.014%). The largest proportion of identified RNAs (34.4%) mapped to non-coding RNA (rfam [51]) with the most abundant species belonging to the Signal Recognition Particle RNA family, universally conserved ribonucleoprotein complexes involved in protein trafficking [52].
10.1080/20013078.2018.1456888-F0008Figure 8.EV RNA profiles as determined by RNA sequencing.
…”
Section: Resultsmentioning
confidence: 99%