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Dot Plots

Dot Plots. DNA dot plots. Identification of regions of Similarity between two sequences Insertions-deletions: Introns Repetitive regions (self-self analysis) ‏ Inverted repeats. Repeats. All DNA sequences contain repeats. Repeats. All DNA sequences contain repeats. Window size.

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Dot Plots

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  1. Dot Plots

  2. DNA dot plots Identification of regions of • Similarity between two sequences • Insertions-deletions: Introns • Repetitive regions (self-self analysis)‏ • Inverted repeats

  3. Repeats • All DNA sequences contain repeats

  4. Repeats • All DNA sequences contain repeats

  5. Window size • Window size 1

  6. Window size • Window size 9

  7. C C T A A A G G G G A A A T C C Exercise Practice for, a) window size 1 b) window size 3 Sequence 2 Sequence 1

  8. C C T A A A G G G G A A A T C C Exercise Window size 1 Identity Sequence 2 Sequence 1

  9. C C T A A A G G G G A A A T C C Exercise Window size 3 Not considered Sequence 2 Sequence 1

  10. C C T A A A G 3 G G G A A A T C C Exercise Window size 3 GGA GGA Sequence 2 = 3 / 3 identities Sequence 1

  11. C C T A A A 2 G 3 G G G A A A T C C Exercise Window size 3 GGA GAA Sequence 2 = 2 / 3 identities Sequence 1

  12. C C T A A 1 A 2 G 3 G G G A A A T C C Exercise Window size 3 GGA AAA Sequence 2 = 1 / 3 identities Sequence 1

  13. C C T A 0 A 1 A 2 G 3 G G G A A A T C C Exercise Window size 3 GGA AAT Sequence 2 = 0 / 3 identities Sequence 1

  14. C C 0 0 0 0 1 3 T 0 0 1 1 3 1 A 0 1 2 3 1 0 A 1 2 3 2 1 0 A 2 3 2 1 0 0 G 3 2 1 0 0 0 G G G A A A T C C Exercise Window size 3 Sequence 2 Sequence 1

  15. Introns } Gene Introns are spliced out in the mRNA } } } mRNA

  16. Protein dot plots

  17. CLC Combined Workbench

  18. Ankyrin repeat protein

  19. HIV Long Terminal Repeats

  20. Di-nucleotide repeats

  21. Repetitive regions

  22. Exercise: Inverted repeats

  23. C C T T T A G G G G A A A T C C Exercise: Inverted repeats Window size 3 Make a dot plot with the sequence against the reverse-complement of the sequence. Now diagonals represent inverted repeats. Reverse complement Sequence 1

  24. Genome dot plots: inverted repeats Analysis of a random sequence of Homo sapiens chromosome 7 reveals numerous short inverted repeats

  25. The human Alu sequence A self-self plot reveals some repetitive regions.

  26. The human Alu sequence A plot of the Alu sequence against its reverse-complement reveals its inverted repeat (palindromic) nature, seen as the diagonal along the entire sequence length

  27. WD-repeat proteins Blosum45 matrix Identity matrix

  28. Conclusion • Dot plots provide an intuitive view of sequence comparisons. • The sliding window size is important. • For proteins, substitution matrices can be used. • Dot plots can reveal • Repeats • Insertion/Deletions (such as introns)‏ • Inverted repeats

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