UCSC Genome Browser

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UCSC Genome Browser

• The God

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What makes UCSC divine?

• Very simple database very powerful output.

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UCSC - overview

• Genome browser
• Tracks
• DNA
• Blat
• Convert

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Detecting AS events cDNAs ESTs
Pre-mRNA
mRNA
EST/cDNA
EST/cDNA aligned to genome
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Identifying alternative splicing events in UCSC

• Constitutive exon
• Exon skipping
• Alt 5
• Alt 3
• Intron Retention
• Mutually exclusive
• Complex events

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Integrating data

• NF1 Pla2G5 Rabl5

How frequent are highly conserved intronic
regions? How significant is lack of SNPs within
800-bp intronic region? Is exonization of
transposable elements a frequent event? Are
secondary structures within exonic/intronic
regions frequent?
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The Prophet

• Galaxy

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Galaxy

• Getting the best out of UCSC
• Supports operations both at the interval level,
  and at the sequence level.
• Lets biologists become bioinformaticians Lets
  bioinformaticians go to the beach.

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Typical workflow in Galaxy

• Extract sets of coordinates either upload from
  computer, or from UCSC table browser.
• Intersect/Subtract different sets of coordinates.
  
• Fetch genomic sequences of coordinates

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Tutorial

• http//www.tau.ac.il/lifesci/bioinfo/teaching/2007
  -2008/Splicing_workshop.htm