Curso Con Ensembl

Browsing Genomes
with Ensembl

www.ensembl.org
www.ensemblgenomes.org

Course Manual v68

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TABLE OF CONTENTS
I) Overview...................................................................................................... 3
II) Introduction to Ensembl....................................................................... 4
III) Walking through the website......................................................... 10
IV) Browsing Ensembl .............................................................................. 26
Exercises ..........................................................................................................26
Answers ............................................................................................................29
V) BioMart(retrieving data) .................................................................. 34
Worked example...........................................................................................34
Exercises ..........................................................................................................39
Answers............................................................................................................43
VI) TASK – Browser + BioMart: ............................................................. 47
A DELETION ON CHROMOSOME 6 ASSOCIATED WITH
MENTAL RETARDATION ..........................................................................47
VII) Exploring Variation data in Ensembl.......................................... 52
Exercises..........................................................................................................52
Answers ............................................................................................................55
VIII) Exploring Regulation data in Ensembl ..................................... 60
Exercises..........................................................................................................60
Answers ............................................................................................................63
IX) Exploring Comparative Genomics data in Ensembl ................ 68
Exercises ..........................................................................................................68
Answers............................................................................................................70
X) Check Your Learning! 10 Advanced Exercises ........................... 74
XI) Quick Guide to Databases and Projects ....................................... 76

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I) Overview

Getting started with Ensembl
www.ensembl.org
Ensembl provides genes and other annotation such as regulatory
regions, conserved base pairs across species, and sequencevariations. The Ensembl gene set is based on protein and mRNA
evidence in UniProtKB and NCBI RefSeq databases, along with
manual annotation from the VEGA/Havana group. All the data are
freely available and can be accessed via the web browser at
www.ensembl.org. Perl programmers can directly access Ensembl
databases through an Application Programming Interface (Perl
API). Gene sequences can bedownloaded from the Ensembl
browser itself, or through the use of the BioMart web interface,
which can extract information from the Ensembl databases without
the need for programming knowledge by the user!

- Data retrieval
with BioMart
- Try our Variant
Effect Predictor

- Search for a gene, clone
location, phenotype,
variation, probeset in any
organism

- Choose your
favouritevertebrate

- Browse plants,
bacteria, fungi, protists
and metazoan at
Ensembl Genomes

You will learn about
 Why do we need genome browsers?
 An introduction to Ensembl
 How information can be obtained from the
site
 An overview of Ensembl tools

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Tired of reading?
Check our video tutorial instead!
http://www.youtube.com/user/Ense
mblHelpdesk
The Ensembl Genome browser...