Training materials

• Ensembl training materials are protected by a CC BY license • http://creativecommons.org/licenses/by/4.0/• If you wish to re-use these materials, please credit Ensembl for

their creation• If you use Ensembl for your work, please cite our papers • http://www.ensembl.org/info/about/publications.html

Ben Moore

Ensembl Outreach Officer

EMBL-EBI

Browsing Genes and Genomes with Ensembl

Objectives

• What is Ensembl?

• What type of data can you get in Ensembl?

• How to navigate the Ensembl browser website.

• How to use Ensembl tools

• Where to go for help and documentation.

This webinar course

Date Webinar topic Instructor

6th April Introduction to Ensembl Helen Sparrow

13th April Ensembl genes Emily Perry

20th April Data export with BioMart Victoria Newman

27th April Variation data in Ensembl and the Ensembl VEP Victoria Newman

4th May Comparing genes and genomes with Ensembl Compara Ben Moore

11th May Finding features that regulate genes – the Ensembl Regulatory Build

Ben Moore

18th May Uploading your data to Ensembl and advanced ways to access Ensembl data

Emily Perry

All webinars begin at 9am BST

Structure

Presentation:What the data/tool isHow we produce/process the data

Demo:Getting the data

Using the tool

Exercises:On the train online course

Questions?

• Ask questions in the Chat box in the webinar interface

• My Ensembl colleagues will respond during

• There’s no threading so please respond with @username

Emily Perry Victoria Newman

Course exerciseshttp://www.ebi.ac.uk/training/online/course/ensembl-browser-w

ebinar-series-2016

This text will be replaced by a YouTube (link to YouKu too) video of this webinar

and a pdf of the slides

The “next page”is the exercises for this

module

A link to exercises and their solutions are in the page hierarchy

Get help with the exercises

• Use the exercise solutions in the online course

• Join our Facebook group and discuss the exercises with everybody (see the online course for the link)

• Email us: helpdesk@ensembl.org

EBI is an Outstation of the European Molecular Biology Laboratory.

Comparative Genomics

Overview of the talk

- Comparative genomics: applications and species- Gene trees- Homology predictions- Whole genome alignments

- pairwise - multiple

- Shared synteny

Applications of Comparative Genomics

Comparative genomics allows us to understand:

- vertebrate evolution

- differences between species at the genome level

- gene function based on homology

- the distribution of highly conserved regions

Comparative analysis by taxa

Ensembl Compara

Ensembl Metazoa Compara

Pan-taxonomic compara

http://www.ebi.ac.uk/~emily/Workshopshttp://ensemblgenomes.org/info/genomes?pan_compara=1

Pan-taxonomic compara

Ensembl Metazoa Compara

Gene trees

- Based on protein alignments - Representative protein of

each Ensembl gene - Clustering, Blast, multiple

alignments- Reconciliation with species

tree - Orthologue/Paralogue

inference

http://www.ensembl.org/info/docs/compara/homology_method.html

Orthologues and Paralogues

Homology relationships

SpeciationDuplication

c1 h1 c2 h2

ParaloguesGenes emerged through a duplication eventegc1 and c2h1 and h2

OrthologuesGenes emerged

through a speciation event

egc1 and h1h2 and mc2 and m

m

One-to-one One-to-many

Hands on

- We’re going to look at a gene BRCA2 to find homologues.

Whole genome alignments

- To identify highly conserved regions- sequences that evolve slowly- regions likely to be functional- both coding and non-coding sequences

- To spot trouble gene predictions

- To define syntenic regions

- Types: pairwise versus multiple

Alignments

- Pairwise alignments with BLASTZ (older) LASTZ-net (newer)

- EPO (Enredo-Pecan-Ortheus) analysis- For selected sets (11 fish, 7 sauropsids, 40 eutherian, 8

primates)

- Mercator-Pecan analysis- For 24 amniota vertebrates (mammals+birds)

http://www.ensembl.org/info/genome/compara/analyses.html#pecan

Shared synteny

http://www.ensembl.org/info/docs/compara/analyses.html

Hands on

- We will look at a human genomic region 2:176087000-176202000 which contains the HoxD cluster to find alignments and conservation regions.

This webinar courseDate Webinar topic Instructor

6th April Introduction to Ensembl Helen Sparrow

13th April Ensembl genes Emily Perry

20th April Data export with BioMart Victoria Newman

27th April Variation data in Ensembl and the Ensembl VEP Victoria Newman

4th May Comparing genes and genomes with Ensembl Compara Ben Moore

11th May Finding features that regulate genes – the Ensembl Regulatory Build Ben Moore

18th May Uploading your data to Ensembl and advanced ways to access

Ensembl data

Emily Perry

Course exercises

http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016

This text will be replaced by a YouTube (link to YouKu too) video of the webinar

and a pdf of the slides.

The “next page” will be the exercises

A link to exercises and their solutions will appear in the page

hierarchy

Get help with the exercises

• Use the exercise solutions in the online course

• Join our Facebook group and discuss the exercises with everybody (see the online course for the link)

• Email us: helpdesk@ensembl.org

Help and documentationCourse online http://www.ebi.ac.uk/training/online/subjects/11

Tutorials www.ensembl.org/info/website/tutorials

Flash animations

www.youtube.com/user/EnsemblHelpdesk

http://u.youku.com/Ensemblhelpdesk

Email us helpdesk@ensembl.org

Ensembl public mailing lists dev@ensembl.org, announce@ensembl.org

Follow us

www.facebook.com/Ensembl.org

@Ensembl

www.ensembl.info

Publications

Aken, BL. et al

Ensembl 2017

Nucleic Acids Research

http://europepmc.org/articles/PMC5210575

Xosé M. Fernández-Suárez and Michael K. SchusterUsing the Ensembl Genome Server to Browse Genomic Sequence Data.Current Protocols in Bioinformatics 1.15.1-1.15.48 (2010)www.ncbi.nlm.nih.gov/pubmed/20521244

Giulietta M Spudich and Xosé M Fernández-SuárezTouring Ensembl: A practical guide to genome browsingBMC Genomics 11:295 (2010)www.biomedcentral.com/1471-2164/11/295

Javier Herrero et al

Ensembl Comparative Genomics Resources

Database (Oxford) 2016: bav096

https://academic.oup.com/database/article-lookup/doi/10.1093/database/bav096

http://www.ensembl.org/info/about/publications.html

Ensembl 2017

Ensembl Acknowledgements

Training materials

• Ensembl training materials are protected by a CC BY license • http://creativecommons.org/licenses/by/4.0/• If you wish to re-use these materials, please credit Ensembl for

their creation• If you use Ensembl for your work, please cite our papers • http://www.ensembl.org/info/about/publications.html