PAG 2019 Workshop: Browsing Genes and Genomes with Ensembl and Ensembl Genomes

Date:

  Sunday 13 January 2019

Venue: 

Town and Country Hotel - 500 Hotel Circle North,  San Diego, , CA,  92108,  United States

Application opens: 

Tuesday 11 December 2018

Application deadline: 

Saturday 12 January 2019

Participation: 

First come, first served

Contact: 

Erin Haskell

Registration fee: 

free

Registration closed

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Dates additional information: 

This workshop forms part of the Genome Annotation Resources at the EBI workshop scheduled from 8:00am until 12:40pm at the Plant and Animal Genomes (PAG) conference. Please see the workshop timetable for further details: https://plan.core-apps.com/pag_2019/event/9441a7255c56cf0ce04b90bfc406932d

Course Overview

'Browsing Genes and Genomes with Ensembl and Ensembl Genomes' will include an introduction to the Ensembl browsers, demonstrate key views in browsing genomes, and show you how to use tools for accessing genomic data and analysing your own, BioMart and the VEP.

Ensembl (www.ensembl.org) provides an interface and an infrastructure for accessing genomic information covering over 130 vertebrate species, including cow, pig, sheep, and chicken. Its sister project, Ensembl Genomes (www.ensemblgenomes.org), consists of five sub-portals (bacteria, protists, fungi, plants, and invertebrate metazoa) which contain data for over 1,000 eukaryotic (including wheat, barley, tomato, brassicas and numerous pathogens) and over 40,000 prokaryotic genomes.

All species in Ensembl and Ensembl Genomes have gene annotation and comparative genomics analyses within the taxa (excluding bacteria). For many of these genomes, we also provide annotation of variants, such as SNPs and CNVs. All these data can be accessed via our browser websites, BioMart (for protists, fungi, plants, and animals), FTP, Perl APIs, REST API, and MySQL. Furthermore, the Variant Effect Predictor (VEP) is a powerful tool for analysing sets of genomic variants, available for all species in Ensembl and Ensembl Genomes.

Audience

All welcome, from wet-lab researchers to bioinformaticians.

 

Learning outcomes

Participants should be able to:

  • View genomic regions and customise the view to add features you are interested in.

  • Explore information about genes and their sequences, and download gene data in bulk using BioMart.

  • Analyse genomic variation data using the VEP.

Programme

  • Introduction to EBI resources and the Ensembl/ Ensembl Genomes genome browsers
  • Exploring genes and genomes using the Ensembl/Ensembl Genomes genome browsers
  • Exporting data with BioMart
  • Analysing variation data with the VEP
  • Wrap-up and questions