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

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


Correct splice site ?


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


“klick”

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

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

visualization of genomic data genome browsers. ucsc browser ensembl browser others ? survey

Documents