visualization of genomic data genome browsers. how many have used a genome browser ? ucsc browser ?...
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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
QuickTime™ and a decompressorare needed to see this picture.
• 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
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