Non-Coding RNA Analysis Using the Rfam Database

Q1 Biochemistry, Genetics and Molecular Biology Current protocols in bioinformatics Pub Date : 2018-06-05 DOI:10.1002/cpbi.51
Ioanna Kalvari, Eric P. Nawrocki, Joanna Argasinska, Natalia Quinones-Olvera, Robert D. Finn, Alex Bateman, Anton I. Petrov
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引用次数: 245

Abstract

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.

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使用Rfam数据库进行非编码RNA分析
Rfam是一个非编码RNA家族数据库,其中每个家族由多序列比对、共识二级结构和协方差模型表示。Rfam结合了手工和基于文献的管理以及定制的软件管道,将科学文献中发现的RNA家族的描述转换为可用于注释任何DNA或RNA序列中属于这些家族的RNA的计算模型。通常锁在图表和补充信息文件中的有价值的研究成果被封装在Rfam条目中,并可通过Rfam网站访问。Rfam产生的数据具有广泛的应用,从基因组注释到为算法开发提供训练集。本文概述了如何搜索和浏览Rfam网站,以及如何用RNA家族注释序列。Rfam数据库可在http://rfam.org免费获得。©2018 by John Wiley &儿子,Inc。
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Current protocols in bioinformatics
Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
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期刊介绍: With Current Protocols in Bioinformatics, it"s easier than ever for the life scientist to become "fluent" in bioinformatics and master the exciting new frontiers opened up by DNA sequencing. Updated every three months in all formats, CPBI is constantly evolving to keep pace with the very latest discoveries and developments.
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