Analysing non-coding RNA with RNAcentral and Rfam

Date:

 Wednesday 11 Thursday 12 September 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Thursday 18 April 2019

Application deadline: 

Friday 23 August 2019

Participation: 

First come, first served

Contact: 

Charlotte Pearton

Registration fee: 

£20

Overview

This workshop, organised in conjunction with the RNA Informatics conference, provides an overview of RNAcentral and Rfam, two databases for non-coding RNA analysis.

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.

Audience

The workshop is aimed at a general audience of biologists and bioinformaticians working with non-coding RNA who are interested in using RNAcentral and Rfam, or for users who would like to bring their projects and discuss them with the RNAcentral and Rfam teams. A basic familiarity with web browsing and an undergraduate level knowledge of molecular biology is recommended for this course. Familiarity with Unix/Linux command line is desirable for part of the course. We recommend these free tutorials:

Syllabus, tools and resources

This workshop provides an overview of two RNA databases developed at EMBL-EBI. RNAcentral is a database of ncRNA sequences that provides a single entry point for accessing all types of ncRNA from a broad range of organisms. RNAcentral provides unified access to ncRNAs data from >30 specialised databases. Rfam is a database of >3,000 RNA families that can be used to identify RNA families in DNA or RNA sequences. Together these resources provide the tools for ncRNA sequence analysis. The goal of the course is to familiarise the audience with the RNAcentral and Rfam websites and demonstrate relevant software, including Infernal and Galaxy.

Outcomes

After this workshop you should be able to:

  • Know when and how to use the RNAcentral and Rfam databases
  • Apply this knowledge to a real-world problem relating to ncRNAs

Additional information

The workshop includes an evening meal at the Hinxton Hall Restaurant on campus, and breaks and lunch outside the EMBL-EBI training rooms.

Programme

Day 1 – Wednesday 11 September 2019
Part 1: Overview of RNAcentral and Rfam
13:30-14:00 Arrival and registration  
14:00-14:30

Introduction to RNAcentral and Rfam

Overview of the websites and data contents

Anton Petrov & Blake Sweeney
14:30-15:30

Exploring ncRNAs in RNAcentral and Rfam practical

Learn how to search for different types of ncRNA data and export information for further processing

Anton Petrov & Blake Sweeney
15:30-15:45 Coffee break  
15:45-18:00

How to use RNAcentral and Rfam with RNA-Seq data practical

Learn how to analyse RNA-Seq datasets using RNAcentral, Rfam, and Galaxy

Blake Sweeney & Ioanna Kalvari
18:00 End of day  
19:00-20:30 Evening meal Hinxton Hall Restaurant
20:30 Shuttle to Cambridge  
Day 2 – Thursday 12 September 2019
Part 2: Problem solving session
08:15 Shuttle to Wellcome Genome Campus  
08:45-09:00 Arrival and registration  
09:00-10:00

How to use Rfam for genome annotation practical

Learn how to use Infernal with Rfam covariance models

Ioanna Kalvari
10:00-10:15 Coffee break  
10:15-12:30

Data surgery

Discuss your research with trainers and other participants. Examples might include:

  • Using Rfam to annotate your dataset of interest with ncRNAs
  • Identifying novel ncRNAs by comparing your data to RNAcentral
  • Contributing new data to Rfam or RNAcentral
Anton Petrov, Blake Sweeney & Ioanna Kalvari
12:30-13:15 Lunch  
13:30 Shuttle to Cambridge