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Visualization of genomic data

Genome browsers. Visualization of genomic data. Survey. UCSC browser Ensembl browser Others ?. UCSC genome browser Basic functionalities used in exercise. Finding a gene by name by sequence Gene structure Orthologues – i.e. functional homolog in other organisms

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Visualization of genomic data

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  1. Genome browsers Visualization of genomic data

  2. Survey • UCSC browser • Ensembl browser • Others ?

  3. UCSC genome browserBasic functionalities used in exercise • 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

  4. Genome browsers Visualization of genomic data

  5. Genome browsersVisualization of a gene Flat files / tab files >chr5:123.004.678-125.345.112 ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGTAA Exon Intron Exon Chr5 123.004.678 123.404.678 124.987.012 125.345.112 Open Reading Frame (ORF) – from start to stop codon

  6. Genome browsersWhy graphic Display ? • Why is a graphic display better than Flat files / tab files • A graphic display is compact • Meta data available i.e. Support information about a gene • Experimental evidence like EST • Predicted gene structures • SNP information • Links to many databases • In short much data about a gene is gathered is one place • and can be viewed easily.

  7. Genome browsersVisualization of a gene (Ensembl)

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

  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. 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…)

  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. Blat genome Browser

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

  17. Logo PlotInformation Content • IC = -H(p) + log2(4) • = a palog2pa + 2 • The Information content is calculated from a multiple sequence alignment. • Result is a graphical visualization of sequence conservation where: • Total height at a position is the Information Content • Height of single letter is proportional to the frequency of that letter • Mutiple alignment of 3 protein sequences: • Seq1: A L R K P Q R T • Seq2: A V R H I L L I • Seq3: A I K V H N N T • Pos1: I = -[1*log2(1)]+ 4.32 = log2(20) = 4.32 • Pos2: I = -[1/3*log2(1/3)+ 1/3*log2(1/3)+ 1/3*log2(1/3)] + 4.32 = 2.73 • Pos3: I = -[2/3*log2(2/3)+ 1/3*log2(1/3) + 4.32 = 3.38

  18. Logo Plot Exon

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

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

  21. Blat genome Browser

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

  23. Genome browsers

  24. Genome browsers

  25. BLAT genome BrowserCenter & zoom

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

  27. BLAT genome BrowserSequence Orthologs

  28. BLAT genome BrowserSequence Orthologs “klick”

  29. BLAT genome BrowserSequence Orthologs

  30. BLAT genome BrowserSequence Orthologs

  31. BLAT genome BrowserSequence Orthologs

  32. SNPs

  33. Single Nucleotide PolymorphismSNP • SNPs can be located anywere in the genome • non synomous (nsSNP) i.e. amino acid is changed (shown below ) • Synomous SNP does not affect the the protein T V I P An amino acid is coded by 3 nucleotides Valine (V): GTC Humans are diploid: cells have 2 homologous copies of each chromosome i.e. 2*23 chromosomes. Haploid cells only 23 chromosomes (sex-cells)

  34. Diploid organism - most mammals An example of two homologous copies of ex chromosome 9 within a cell A chromosome from mother A chromosome from father If the red strand is the plus-strand: C;T (or T;C but we write it alphabetical) If the green strand is the minus strand: G;A but we write it as G;A

  35. SNPs

  36. SNPs

  37. Exercise Basic understanding of the graphics Effect of Single Nucleotide Polymorphisms (SNPs) Finding Orthologue genes Identify chromosomal locus for a gene

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