scholarly journals Non-Coding RNA Analysis Using the Rfam Database

2018 ◽  
Vol 62 (1) ◽  
pp. e51 ◽  
Author(s):  
Ioanna Kalvari ◽  
Eric P. Nawrocki ◽  
Joanna Argasinska ◽  
Natalia Quinones-Olvera ◽  
Robert D. Finn ◽  
...  
Keyword(s):  
Rfam Database ◽  
Rna Analysis ◽  
Non Coding Rna

scholarly journals Highly Divergent Neuropeptide - non-coding RNA regulatory networks underpin variant host-finding behaviours in Steinernema species infective juveniles

2020 ◽  
Author(s):  
Neil D. Warnock ◽  
Erwan Atcheson ◽  
Ciaran McCoy ◽  
Johnathan J. Dalzell
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Regulatory Networks ◽  
Host Finding ◽  
Protein Coding ◽  
Rna Analysis ◽  
New Family ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Shared Gene

AbstractWe conducted a transcriptomic and small RNA analysis of infective juveniles (IJs) from three behaviourally distinct Steinernema species. Substantial variation was found in the expression of shared gene orthologues, revealing gene expression signatures that correlate with behavioural states. 97% of predicted microRNAs are novel to each species. Surprisingly, our data provide evidence that isoform variation can effectively convert protein-coding neuropeptide genes into non-coding transcripts, which may represent a new family of long non-coding RNAs. These data suggest that differences in neuropeptide gene expression, isoform variation, and small RNA interactions could contribute to behavioural differences within the Steinernema genus.

scholarly journals rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245280
Author(s):  
Lara Sellés Vidal ◽  
Rafael Ayala ◽  
Guy-Bart Stan ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
R Package ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Rfam Database ◽  
Non Coding Rna ◽  
Covariance Models ◽  
Available Information ◽  
Client Side ◽  
Programmatic Access

rfaRm is an R package providing a client-side interface for the Rfam database of non-coding RNA and other structured RNA elements. The package facilitates the search of the Rfam database by keywords or sequences, as well as the retrieval of all available information about specific Rfam families, such as member sequences, multiple sequence alignments, secondary structures and covariance models. By providing such programmatic access to the Rfam database, rfaRm enables genomic workflows to incorporate information about non-coding RNA, whose potential cannot be fully exploited just through interactive access to the database. The features of rfaRm are demonstrated by using it to analyze the SARS-CoV-2 genome as an example case.

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