rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families
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Publication available at
Author(s)
Selles Vidal, L
Ayala, R
Stan, G-B
Ledesma-Amaro, R
Type
Journal Article
Abstract
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.
Date Issued
2021-01-15
Online Publication Date
2021-03-08T14:00:26Z
Date Acceptance
2020-12-27
ISSN
1932-6203
Publisher
Public Library of Science (PLoS)
Journal / Book Title
PLoS One
Volume
16
Issue
1
Copyright Statement
© 2021 Sellés Vidal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
License URI
Sponsor
Biotechnology and Biological Sciences Research Council (BBSRC)
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000609991600009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
BB/T011408/1
Subjects
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Databases, Genetic
Humans
RNA, Untranslated
RNA, Viral
SARS-CoV-2
Sequence Analysis, RNA
Software
Humans
RNA, Untranslated
RNA, Viral
Sequence Analysis, RNA
Software
Databases, Genetic
SARS-CoV-2
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
General Science & Technology
Publication Status
Published
Article Number
ARTN e0245280
Date Publish Online
2021-01-15