Exploring Non-Coding RNAs in RNAcentral

Q1 Biochemistry, Genetics and Molecular Biology

Current protocols in bioinformatics Pub Date : 2020-08-26 DOI:10.1002/cpbi.104

Blake A. Sweeney, Arina A. Tagmazian, Carlos E. Ribas, Robert D. Finn, Alex Bateman, Anton I. Petrov

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引用次数: 3

Abstract

Non-coding RNAs are essential for all life and carry out a wide range of functions. Information about these molecules is distributed across dozens of specialized resources. RNAcentral is a database of non-coding RNA sequences that provides a unified access point to non-coding RNA annotations from >40 member databases and helps provide insight into the function of these RNAs. This article describes different ways of accessing the data, including searching the website and retrieving the data programmatically over web APIs and a public database. We also demonstrate an example Galaxy workflow for using RNAcentral for RNA-seq differential expression analysis. RNAcentral is available at https://rnacentral.org. © 2020 The Authors.

Basic Protocol 1: Viewing RNAcentral sequence reports

Basic Protocol 2: Using RNAcentral text search to explore ncRNA sequences

Basic Protocol 3: Using RNAcentral sequence search

Basic Protocol 4: Using RNAcentral FTP archive

Support Protocol 1: Using web APIs for programmatic data access

Support Protocol 2: Using public Postgres database to export large datasets

Support Protocol 3: Analyze non-coding RNA in RNA-seq datasets using RNAcentral and Galaxy

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探索rnaccentral中的非编码rna

非编码rna对所有生命都是必不可少的，并具有广泛的功能。关于这些分子的信息分布在几十个专门的资源中。RNAcentral是一个非编码RNA序列数据库，它为来自40个成员数据库的非编码RNA注释提供了一个统一的访问点，并有助于深入了解这些RNA的功能。本文描述了访问数据的不同方法，包括通过web api和公共数据库以编程方式搜索网站和检索数据。我们还演示了一个使用RNAcentral进行RNA-seq差异表达分析的示例Galaxy工作流。RNAcentral可在https://rnacentral.org上获得。©2020作者。基本协议1:查看RNAcentral序列报告基本协议2:使用RNAcentral文本搜索探索ncRNA序列基本协议3:使用RNAcentral文本搜索基本协议4:使用RNAcentral FTP归档支持协议1:使用web api进行程序化数据访问支持协议2:使用公共Postgres数据库导出大型数据集支持协议3:使用RNAcentral和Galaxy分析RNA-seq数据集中的非编码RNA

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Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

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