1. Sequence Analysis
Alan Christoffels

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

3. 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

4. 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

5. 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

6. 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

7. What is a sequence alignment??
S O U T H A F R I C A
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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

8. 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
gap
S O U T H A F R I C A
S O U T - A F R I C A

9. 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

10. Gaps, Insertions & deletions (indels) and substitutions
S O U T H A F R I C A
S O U T H R I K A N
gaps

12. End-to-end
Not aligned

13. Why do we want to compare sequences??
Predict functions of unknown sequences; find gene families

14. Why do we want to compare sequences??
What is underlying hypothesis when you predict a function by comparing two sequences ?????
Predict functions of unknown sequences; find gene families

15. Why do we want to compare sequences??
Predict functions of unknown sequences; find gene families

16. Why do we want to compare sequences??
Predict functions of unknown sequences; find gene families
Positions not critical to function can mutate randomly!!!!!

17. Why do we want to compare sequences??
Predict functions of unknown sequences; find gene families
Find an example where the above is not necessarily true

18. Sequence Comparisons similarity due to a common ancestor
Homology
similarity due to a common ancestor
no degrees of homology
Predict functions of unknown sequences; find gene families

19. Sequence Comparisons
Predict functions of unknown sequences; find gene families

20. Sequence Comparisons
Predict functions of unknown sequences; find gene families

21. Sequence Comparisons
Predict functions of unknown sequences; find gene families

22. Sequence Comparisons
Predict functions of unknown sequences; find gene families

23. Sequence Comparisons Dot-plots
Predict functions of unknown sequences; find gene families

24. Dot - plots
One sequence compared to another. Identify regions of similarity

25. Dot - plots
One sequence compared to another. Identify regions of similarity

26. One sequence compared to another. Identify regions of similarity

34. What do palindromes look like in a dot-plot????

42. Scoring Path