Online database resources for non-coding RNA

Date:

  Wednesday 17 June 2015

Venue: 

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

Application deadline: 

Wednesday 10 June 2015

Participation: 

First come, first served

Contact: 

Johanna Langrish

Registration fee: 

£55.00

Registration closed

Overview

Knowledge about non-coding RNAs is spread across a wide range of websites and it can be difficult for new users to understand which resources provide relevant data. This one-day course focuses on four online data resources for non-coding RNAs. The course will introduce users to RNAcentral, a comprehensive resource of non-coding RNA sequences, miRBase which is dedicated to microRNAs, GENCODE which supplies detailed expertly curated gene sets for human and mouse, and Rfam which annotates genomes with matches to non-coding RNA families. The course will contain a mixture of short presentations and practical challenges.

Audience

The course is targeted at biologists either working on non-coding RNAs or interested in working with them. Users require only a basic familiarity with web browsing and an understanding of basic molecular biology.

Syllabus, tools and resources

During this course you will learn about:

  • RNAcentral – a comprehensive ncRNA sequence database
  • miRBase – the authoratative microRNA database
  • GENCODE – the curated long non-coding RNA human/mouse gene sets
  • Rfam – the database of RNA families and motifs

Outcomes

After this course you should be able to:

  • Understand the types of ncRNA data that are available
  • Be aware of the uses of different RNA resources and databases
  • Search RNA databases for information on particular RNA genes and families
  • Perform sequence similarity searches for ncRNAs
  • Access lncRNA data in genome browsers (UCSC, Ensembl) and view the latest manually curated lncRNAs in Vega
  • Know how to contribute data to ncRNA databases and resources

Programme

Time Topic Trainer
Day 1 - Wednesday 17th June 
09:00 - 09:30 Coffee and registration  
09:30 - 10:00 An introduction to RNA informatics Anton Enright
10:00 - 10:30 RNAcentral introduction Anton Petrov 
10:30 - 11:15 RNAcentral exercises  Anton Petrov  
11:15 - 11:30 Tea/coffee break 
11:30 - 12:00 GENCODE introduction  Jen Harrow 
12:00 - 12:45 IncRNA exercises Jen Harrow 
12:45 - 13:45 Lunch 
13:45 - 14:15 miRBase introduction Sam Griffiths-Jones
14:15 - 15:00 miRBase exercises Sam Griffiths-Jones  
15:00 - 15:15 Tea/coffee break  
15:15 - 15:45 Rfam introduction  Alex Bateman 
15:45 - 16:30 Rfam exercises  Alex Bateman
16:30 - 17:00 Concluding remarks & Online Survey
17:15 Coach departing from the EBI for the journey to Cambridge Train Station (approx 45mins journey)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

 

Registration is now closed

The registration fee for this course is £55.00, which includes:

  • Refreshments and lunch throughout the day
  • Course materials
  • Use of the EBI Training Room computer for the duration of the course
  • Coach from The EBI to Cambridge Train Station at the end of the course

Departures - A coach is booked to take participants from The EBI to Cambridge Train Station at the end of the course - (from Cambridge, participants will be able to take the train to all main line train stations).

There will be a maximum of 30 participants on this course.

This course has been kindly supported by BBSRC.

Application deadline

10 June 2015

Number of places

30 places

Registration closed

Organisers

Anton Petrov

Trainers

Alex Bateman - EMBL-EBI, UK

Anton Petrov - EMBL-EBI, UK

Jen Harrow - Welcome Trust Sanger Institute, UK

Sam Griffiths-Jones - The University of Manchester, UK