Genome browsers Visualization 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 browser Basic 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 Browser
http://genome.ucsc.edu//
BLAT genome Browser
Using a search term or position eg Chr1:10,234-11,567
BLAT genome Browser
http://genome.ucsc.edu/
BLAT genome Browser
Using a protein or DNA sequence
BLAT Blast 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 site
exon... . G | GT ...intron ...AG | exon...
Blat genome Browser
BLAT genome Browser ”Browser”
Base,
Center &
Zoom Known genes Predictions RNA EST Conservation Expression
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