Non-Coding RNA Analysis Using the Rfam Database

Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA f...

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Vydáno v:Current protocols in bioinformatics Ročník 62; číslo 1; s. e51
Hlavní autoři: Kalvari, Ioanna, Nawrocki, Eric P, Argasinska, Joanna, Quinones-Olvera, Natalia, Finn, Robert D, Bateman, Alex, Petrov, Anton I
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 01.06.2018
Témata:
Base Sequence
Databases, Nucleic Acid
Genome, Human
Humans
Molecular Sequence Annotation
Nucleic Acid Conformation
Riboswitch - genetics
RNA, Untranslated - chemistry
RNA, Untranslated - genetics
Sequence Alignment
Sequence Analysis, RNA
RNA family
non-coding RNA
genome annotation
Infernal
Rfam
ISSN:1934-340X, 1934-340X
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Shrnutí:Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org. © 2018 by John Wiley & Sons, Inc.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1934-340X
1934-340X
DOI:10.1002/cpbi.51