T5 – Delving into non-coding RNA with RNAcentral and Rfam
Date: September 8th
Time: 9:00 – 16:00
- Dr Anton Petrov, EMBL-EBI https://www.ebi.ac.uk/about/people/anton-petrov
- Ioanna Kalvari, EMBL-EBI https://www.ebi.ac.uk/about/people/ioanna-kalvari
Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins and are found in every living organism. Many ncRNAs are responsible for important biological functions. For example, rRNA is a key component of the ribosome, and microRNAs regulate gene expression. Researchers from different fields of Biology may need to find what is known about specific ncRNA or identify ncRNA in their data but may not have the required expertise.
In this tutorial we will give an overview of RNAcentral and Rfam, two complementary resources dedicated to ncRNA. RNAcentral (http://rnacentral.org) is a database of ncRNA sequences that provides a single entry point for accessing ncRNA sequences of all types from a broad range of organisms. Rfam (http://rfam.org) is a database of over 2,600 ncRNA families that can be used to identify RNA families in DNA or RNA sequences. Together these resources provide important tools for ncRNA sequence analysis.
The goal of the tutorial is to familiarise the audience with the RNAcentral and Rfam websites, and demonstrate relevant software, such as Infernal (http://eddylab.org/infernal).
The tutorial is aimed at a general audience of biologists and bioinformaticians- working with non-coding RNA. A basic familiarity with web browsing and an undergraduate level knowledge of basic molecular biology is recommended for this course. Familiarity with Unix/Linux command line is desirable for part of the course. Different types of hands-on exercises will be provided for different levels of users.
|Part 1: RNAcentral|
|09:00 ‒ 09:30||Introduction to RNAcentral
Overview of RNAcentral and its data
|09:30 ‒ 10:30||Exploring ncRNA in RNAcentral
Learn to search for different types of ncRNA data in RNAcentral and export information for further processing Hands-on exercises
|10:30 ‒ 10:45||Coffee break|
|10:45 ‒ 11:45||Identifying novel ncRNAs using RNAcentral Comparing sequencing datasets with RNAcentral to identify novel ncRNA transcripts. Hands-on exercises|
|11:45 ‒ 12:00||Questions and discussion|
|12:00 ‒ 13:00||Lunch break|
|Part 2: Rfam|
|13:00 ‒ 13:30||Introduction to Rfam
Overview of Rfam and RNA families
|13:30 ‒ 14:30||Navigating the Rfam website
Explore RNA families and precomputed genome annotations
|14:30 ‒ 14:45||Coffee break|
|14:45 ‒ 15:45||Annotating genomes with RNA families using Infernal This section will demonstrate how to use Infernal software. Hands-on exercises|
|15:45 ‒ 16:00||Questions and end of program|
The participants are expected to use their own laptops. Internet access will be required.