Access to Genes and Genomes with Ensembl
www.ensembl.org
www,ensemblgenomes.org
The Ensembl and Ensembl genomes projects provide comprehensive and
integrated sources of genome annotation. This workshop offers participants the
possibility of gaining hands-on experience in the use of the Ensembl genome
browser and provides them with the necessary background information. Primarily
targeted at wetlab scientists, a combination of hands-on exercises along with
presentations will lead the scientist through tools and annotation he/she may be
able to use in the course of biological research.
The workshop consists of the following modules. Most modules consist of a
presentation, followed by the opportunity to do exercises.
Morning
* Introduction to Ensembl : origin, goals and organization of the Ensembl
project
* Worked example: guided tour of the most important pages of the Ensembl
website including variation and comparative genomics data
* Data mining with BioMart: retrieving datasets using the data mining tool
BioMart
Afternoon Modules (for a 1-day course)
* More on comparative genomics and proteomics: orthologues, protein families,
whole genome alignments and syntenic regions
* More on variations: SNP (Single nucleotide polymorphisms), InDels and
CNVs in Ensembl, disease and phenotypes associated with sequence variations,
structural variations, and comparison of strains (mouse), breeds (dogs),
individuals (humans) using the browser and BioMart. Prediction of allele
consequences on transcripts using the Variant Effect Predictor.
* Focus on regulatory regions in the genome based on ENCODE data.