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

2. Why Compare Sequences?

4. 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

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

11. 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. 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

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. 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 gap

16. 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 Uncertainty in Alignments

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

18. Global vs. Local Alignment

19. End-to-end

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

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

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

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

24. Dynamic Programming

28. Note the Repeats

29. Dynamic Programming Repeats

30. Dynamic Programming Repeats

31. Dynamic Programming 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