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Using the Ensembl Genome browser

 

Description

The Ensembl Projectprovides a comprehensive and integrated source of annotation of mainly vertebrate and genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information.

This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.

There may be some tools and topics that do not apply to non-vertebrates. If you have any questions about this, please email the Ensembl Outreach Project Leader, Emily Perry.

 

Trainers

Denise Carvalho-Silva, EMBL-EBI

 

Audience and Prerequisites

  • Knowledge of basic genetics and basic bioinformatics terminology is very helpful for this course
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals. 

 

Syllabus, Tools and Resources

During this course you will learn about:

  • Introduction to Ensembl: origin, goals and organization of the Ensembl project
  • Worked example: guided tour of the most important pages of the Ensembl website
  • Data mining with BioMart: retrieving datasets using the data mining tool BioMart
  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
  • Variation: SNPs and other polymorphisms, haplotypes, linkage disquilibrium, structual variants like CNVs

 

Learning Objectives

After this course you should be able to:

  • Access and navigate the Ensembl homepage
  • Search the Ensembl browser with a gene, location (a region of a genome), or polymorphism of interest
  • Understand the different ways the results are presented in Ensembl (including the gene, location, transcript and variation tabs)
  • Export Ensembl data quickly and easily with the browser and BioMart

 

Links

Book Here

Ensembl training materials

 

Timetable

Time Topic
9:30 - 12:30 Introduction to Ensembl and Ensembl genes
Viewing genes and locations in the browser
Data-mining with BioMart
12:30 - 13:30  Lunch
13:30 - 17:30 Genetic variation, comparative genomics or gene regulation, depending on participants' interests
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