T5 – Delving into non-coding RNA with RNAcentral and Rfam

 

Tutorial Details

Date: September 8th

Time: 9:00 – 16:00

Venue: Stavros Niarchos Foundation Cultural Center

Room: B_VIP_1st

 

Tutors

Summary

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).

 

Target audience

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.

 

Schedule

Time Topic
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

Hands-on exercises

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

 

Requirements

The participants are expected to use their own laptops. Internet access will be required.