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Tutorial 12

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

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  1. Tutorial 12 Genome browser

  2. 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.

  3. Genome browser http://genome.ucsc.edu/

  4. How to find a gene of interest?

  5. genome Genome assembly location Gene name OR

  6. Lets take a look at the gene

  7. Information about the gene Sequences +Links to other databases

  8. Expression data Structural information

  9. RNA secondary structure

  10. Basic tracks

  11. RefSeq id Other names Summary on the gene Genomic position Gene length Sequences

  12. mRNA length Protein sequence, mRNA sequence

  13. Conservation

  14. Zoom in to compare base level

  15. Zooming in can help us identifying alternative splicing events

  16. Additional tracks

  17. Literature track

  18. RNA-Seq and regulation

  19. Common SNPs

  20. Tables

  21. How to download a gene sequence?

  22. Clade, genome, assembly Group and track “Known genes” table position Choose “sequence”

  23. Different parts of the gene

  24. Other possible tracks from the table browser

  25. miRNAs in the human genome

  26. Adding custom tracks

  27. browser position chr17:41243452-41277500 track name=unknown description="unknown genomic element" color=255,0,0, chr17 41244000 41246000

  28. Here’s our custom track! http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

  29. BLAT

  30. 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

  31. : :

  32. Examples

  33. 1. In which chromosome can you find the CFTR gene in human?

  34. 2. In which chromosome can you find the CFTR gene in mouse?

  35. 3. How many exons does the CFTR gene have?

  36. 4. Which genes are close to CFTR on chromosome 7? Zooming out

  37. 5. What is the orientation of the gene? Plus or minus?

  38. 6. download the promoter area of the CFTR gene (1000 bp)

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