Using the Ensembl Genome Browser BeginnersPrerequisites
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, 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.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.
- The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users
- Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
- Further details regarding eligibility criteria are available here
- Further details regarding the charging policy are available here
- Basic computing skills
- Graduate level in Life Sciences
- Knowledge of basic genetics and basic bioinformatics terminology is very helpful for this course
Number of sessions: 1
| # | Date | Time | Venue | Trainers | |
|---|---|---|---|---|---|
| 1 | Fri 27 Nov 2015 09:30 - 17:00 | 09:30 - 17:00 | Bioinformatics Training Room, Craik-Marshall Building | map | Denise Carvalho-Silva, Helen Sparrow |
- 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
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
During this course you will learn about:
- the data types in Ensembl
- how to view data in the Ensembl browser
- how to mine Ensembl data using BioMart
Presentations, demonstrations and practicals
Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl
1
A number of times per year
Booking / availability