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Tutorial 12. Genome browser. Genome browser. Free, open source, online browser for genomes. Contains ~100 genomes, from nematodes to human. Many tools that can be used to analyze genomic data. Genome browser. http://genome.ucsc.edu/. How to find a gene of interest?. genome.
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Tutorial 12 Genome browser
Genome browser • Free, open source, online browser for genomes. • Contains ~100 genomes, from nematodes to human. • Many tools that can be used to analyze genomic data.
Genome browser http://genome.ucsc.edu/
genome Genome assembly location Gene name OR
Information about the gene Sequences +Links to other databases
Expression data Structural information
RefSeq id Other names Summary on the gene Genomic position Gene length Sequences
mRNA length Protein sequence, mRNA sequence
Zooming in can help us identifying alternative splicing events
Clade, genome, assembly Group and track “Known genes” table position Choose “sequence”
browser position chr17:41243452-41277500 track name=unknown description="unknown genomic element" color=255,0,0, chr17 41244000 41246000
Here’s our custom track! http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
BLAT • BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. • BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all overlapping 11-mers stepping by 5. • Protein BLAT works in a similar manner
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4. Which genes are close to CFTR on chromosome 7? Zooming out