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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)