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Sequence Analysis

Sequence Analysis. Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST). Why Compare Sequences?. Why Compare Sequences?. Why Compare Sequences?. Positions not critical to function can mutate randomly!!!!!. Sequence Comparisons. Homology

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Sequence Analysis

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  1. Sequence Analysis • Alignments • dot-plots • scoring scheme • Substitution matrices • Search algorithms (BLAST)

  2. Why Compare Sequences?

  3. Why Compare Sequences?

  4. Why Compare Sequences? Positions not critical to function can mutate randomly!!!!!

  5. Sequence Comparisons • Homology • similarity due to a common ancestor • no degrees of homology • Paralogy • Orthology Homework: Define para/ ortholog

  6. Sequence Comparisons

  7. Sequence Comparisons

  8. Sequence Comparisons

  9. Sequence Comparisons

  10. What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A

  11. What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A

  12. What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A

  13. S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A What is a Sequence Alignment?

  14. What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A S O U T H A F R I C A S O U T - A F R I C A

  15. gap S O U T H A F R I C A S O U T H A F R I K A S O U T H A F R I C A S O U T - A F R I C A What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A

  16. Uncertainty in Alignments S O - T H A F R I C A S O O T H - F R I K A N S - O T H A F R I C A S O O T H - F R I K A N

  17. Gaps, Insertions, Deletions (Indels) & Substitutions substitution S O U T H A F R I C A S O U T H - - R I K A N gaps

  18. Global vs. Local Alignment

  19. End-to-end Global vs. Local Alignment

  20. End-to-end Not aligned Global vs. Local Alignment Homework: Define

  21. End-to-end Not aligned Global vs. Local Alignment Homework: When do you use which?

  22. Dot Plots Dot-plot of a sequence against itself

  23. More dot plot examples Insertion/ Deletion Internal Repeats Divergence Homework: What do palindromes look like in a dot-plot?

  24. Dynamic Programming

  25. Dynamic Programming

  26. Dynamic Programming

  27. Dynamic Programming

  28. Dynamic Programming Note the Repeats Note the Repeats

  29. Dynamic Programming Repeats

  30. Dynamic Programming Repeats

  31. Dynamic Programming Repeats Repeats

  32. Which Alignment is Best? www.wellesley.edu/CS/courses/CS-BiSc303/slides/alignment.pdf

  33. Which Alignment is Best? www.wellesley.edu/CS/courses/CS-BiSc303/slides/alignment.pdf

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