Visualization of genomic data

Genome browsers

• How many have used a genome browser ?

• UCSC browser ?

• Ensembl browser ?

• Others ?

survey

Visualization of genomic data

Genome browsers

Genome browsersVisualization of a gene

>sequenceATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGCGTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCGAAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGACTGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGCACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCTGTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAGGGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACACGCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTTAGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA

Chr5 123.004.678 123.404.678 124.987.012 125.345.112

Flat files / tab files

Genome browsersVisualization of a gene (Ensembl)

Genome browsersVisualization of a gene (UCSC)

Exon Intron UTR

Genome browsers

Genome browsers

• UCSC genome browser

• http://genome.ucsc.edu/

• Easy to use

• Often updates, but not as often as Ensembl

• upload of personal tracks

• Ensembl browser

• http://www.ensembl.org/index.html

• Less easy to use

• Maintained/updated by several people

• Gbrowser

• http://www.gmod.org/GBrowse

Genome browsers

UCSC genome browserBasic functionalities

• Finding a gene

• by name

• by sequence

• Gene structure

• Sequence orthologues

• Single Nucleotide Polymorphisms

• Gene Sorter - sort according to expression, homology ...

• Custom tracks

BLAT genome Browserhttp://genome.ucsc.edu//

BLAT genome Browser

Using a search term or position eg Chr1:10,234-11,567

BLAT genome Browserhttp://genome.ucsc.edu/

BLAT genome Browser

Using a protein or DNA sequence

BLATBlast Like Alignment Tool

• BLAT (2002)

• Very fast searches (MySQL database)

• Handle introns in RNA/DNA alignments

• Data for more that 30 genomes (human, mouse, rat…)

Exon Intron Exon

Splice sites

Blat genome Browser

BLAT genome Browser”Details”

Correct splice site ?

BLAT genome Browser”Details”

Donor site | Acceptor siteexon... . G | GT ...intron ...AG | exon...

Blat genome Browser

BLAT genome Browser”Browser”

Base,Center &ZoomKnown genes

Predictions

RNA

EST

Conservation

Expression

BLAT genome BrowserCenter & zoom

BLAT genome BrowserCenter & zoom

Forward/reverse direction

Selected number of tracks

BLAT genome BrowserSequence Orthologs

BLAT genome BrowserSequence Orthologs

“klick”

BLAT genome BrowserSequence Orthologs

BLAT genome BrowserSequence Orthologs

BLAT genome BrowserSequence Orthologs

SNPs

SNPs

Chromosomal locus

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• A locus is a physical location on a chromosome• p the ‘short arm’• q the ‘long arm’• A locus range may describe a location of a gene

• 22q11.21-q11.23

22q12.2

Chromosome 22Arm qBand 12Sub-band 2

Chromosomal locusSearching with gene name

Chromosomal locusSearching with locus range

Custom tracks

• Upload your personal data• Share data with colleagues

• Data need to be related to a reference organism

Custom tracks

Custom tracks

Exercise

1. Basic understanding of the graphics2. Effect of Single Nucleotide Polymorphisms (SNPs)3. Finding Orthologue genes4. Identify chromosomal locus for a gene