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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
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
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”Browser”
Base,Center &ZoomKnown genes
Predictions
RNA
EST
Conservation
Expression
Custom tracks
• Upload your personal data• Share data with colleagues
• Data need to be related to a reference organism