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Visualization of genomic data

Genome browsers. Visualization of genomic data. survey. How many have used a genome browser ? UCSC browser ? Ensembl browser ? Others ?. Genome browsers. Visualization of genomic data. Genome browsers Visualization of a gene. Flat files / tab files. >sequence

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Visualization of genomic data

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  1. Genome browsers Visualization of genomic data

  2. survey • How many have used a genome browser ? • UCSC browser ? • Ensembl browser ? • Others ?

  3. Genome browsers Visualization of genomic data

  4. Genome browsersVisualization of a gene Flat files / tab files >sequence ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA Chr5 123.004.678 123.404.678 124.987.012 125.345.112

  5. Genome browsersVisualization of a gene (Ensembl)

  6. Genome browsersVisualization of a gene (UCSC) Exon Intron UTR

  7. Genome browsers

  8. Genome browsers

  9. 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

  10. UCSC genome browserBasic functionalities • Finding a gene • by name • by sequence • Gene structure • Sequence orthologues • Single Nucleotide Polymorphisms • Gene Sorter - sort according to expression, homology ... • Custom tracks

  11. BLAT genome Browser http://genome.ucsc.edu//

  12. BLAT genome Browser Using a search term or position eg Chr1:10,234-11,567

  13. BLAT genome Browser http://genome.ucsc.edu/

  14. BLAT genome Browser Using a protein or DNA sequence

  15. Splice sites Exon Intron Exon BLATBlast 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…)

  16. Blat genome Browser

  17. BLAT genome Browser”Details” Correct splice site ?

  18. BLAT genome Browser”Details” Donor site | Acceptor site exon... . G | GT ...intron ...AG | exon...

  19. Blat genome Browser

  20. BLAT genome Browser”Browser” Base, Center & Zoom Known genes Predictions RNA EST Expression Conservation

  21. BLAT genome BrowserCenter & zoom

  22. BLAT genome BrowserCenter & zoom Selected number of tracks Forward/reverse direction

  23. BLAT genome BrowserSequence Orthologs

  24. BLAT genome BrowserSequence Orthologs “klick”

  25. BLAT genome BrowserSequence Orthologs

  26. BLAT genome BrowserSequence Orthologs

  27. BLAT genome BrowserSequence Orthologs

  28. SNPs

  29. SNPs

  30. Gene Sorter

  31. Gene Sorter - homology Closest homologues

  32. Custom tracks • Upload your personal data • Share data with colleagues • Data need to be related to a reference organism

  33. Custom tracks

  34. Custom tracks

  35. Exercise Basic understanding of the graphics Effect of Single Nucleotide Polymorphisms (SNPs) Finding Orthologue genes http://www.cbs.dtu.dk/courses/humanbio/2009/exercises/ExGenomeBrowser/ExGenomeBrowser.pdf

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