Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.

Visualization of genomic data

Genome browsers

•UCSC browser

• Ensembl browser

• Others ?

Survey

UCSC genome browserBasic functionalities

• Finding a gene

• by name

• by sequence

• Gene structure

• Orthologues – i.e. functional homolog in other organisms

• SNP’s - Single Nucleotide Polymorphisms

• Several other functionalities

• Gene Sorter - sort according to expression, homology, in situ images of genes in different tissues

• Custom tracks – upload your own data

• 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

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

Exon

Exon

Intron

Genome browsersVisualization of a gene (Ensembl)

Genome browsersVisualization of a gene (UCSC)

Exon Intron UTR

Header

Genome browsers

Genome browsers

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 genomic 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 ?

Splice sites

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

Gene Sorter

Gene Sorter - homology

Closest homologues

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 genes

http://www.cbs.dtu.dk/courses/humanbio/2009/exercises/ExGenomeBrowser/ExGenomeBrowser.pdf