Genome Browsers

Carsten O. Daub

Omics Science Center

RIKEN, Japan

May 2008

Outline

• Give some impression of the intuitive handling of the browsers

• Highlight some of the specific functions

• Point out some of the strengths of the different browsers

General comments

• We will focus on two genome growsers in this lecture

• UCSC genome browser

• ENSEMBL genome browser

• Some comments about the RIKEN FANTOM3 genome browser

General comments cont’d.

• The genome browsers are parts of bigger genome information resources

• Their main purpose is to graphically display complex information

• And to put this information into the genomic context

• We will not discuss all of the rich functionalities of UCSC and ENSEMBL here

General comments cont’d.

• Genome browsers are tools to – display various types of information – in the context of the genome

The context of the genome

• Graphical representation of the genome

• The chromosomes are displayed as straight ’strings’

• With coordinates for the positions

• Various features are aliged to the chromosomes and displayed as tracks

What information is displayed?

• Which features can be displayed in such a way?

• Which features NOT?

UCSC genome browser

chr7

Mouseover effect

Zoom in

Tracks

Comments on Gene models

Some comments on gene models:• different databases have different ways to define gene models

Common examples are• NCBI: RefSeq, ’Known genes’• ENSEMBL: Known genes, Novel genes, Predicted genes

• What are the differences of the models?• Which one is the better model?

stat3

Tracks in the Genome Browser

• Various types of information are aligned to the genome in groups, so calles tracks

• Each track contains a logical unit of information– Different gene models– Experimental evidence: cDNA, mRNA, EST– Expression and regulation– Repeats, SNPs, miRNA, ...– Comparative genomics

Customizing tracks

• Tracks can be displayed in different levels of detail

dense

FULL

Upload your own track

• You can upload your own track to the genome browser– As a file– As a URL pointing to a file– Data must be formatted in BED, GFF, GTF,

WIG or PSL formats.

• Example: – You want to display miRNA target predictions

in the genome browser

Export as high quality graphic

• It can be important, for example for a publication, to obtain high quality versions of the graphs displayed in the genome browser

Customizing the display

• Many details about the display can be customized

UCSC genome browser as data repository

• The genome browser is the front-end of a data repository

• The backend is a database that contains all the details about the displayed information

• The information in the databases can be retrieved seperately from the download section

ENSEMBL• About the Ensembl Project• Ensembl is a joint project between EMBL -

European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust.

• Goals of Ensembl• The Ensembl project aims to provide: • Accurate, automatic analysis of genome data. • Analysis and annotation maintained on the current data. • Presentation of the analysis to all via the web. • Distribution of the analysis to other bioinformatics laboratories.

stat3

Summary

• The UCSC browser and the ENSEMBL browser have very similar functions

• It needs some time to get accustomed to any of them

• Remommendation: – Choose one of them– Get used to it– Stick to it

Summary cont’d

• They are highly flexible

• They allow to easily get an impression of a genomic region

• They are extremely powerful tools for – beginners as well as for experts– For biologists as well as Bioinformaticians

RIKEN Genomic Elements Viewer

• RIKEN provides the genomic elements viewer

• It was specifically developed to display the RIKEN CAGE data

• CAGE data provides infoemation about the start of a transcript

• And is very valuable for e.g.– Promoter analysis– Alternative regulation (isoforms)