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Sequence Analysis Alan Christoffels alan@sanbi.ac.za

Sequence Analysis Alan Christoffels alan@sanbi.ac.za. Sequence Analysis Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST). 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. What is a sequence alignment??.

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Sequence Analysis Alan Christoffels alan@sanbi.ac.za

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  1. Sequence Analysis Alan Christoffels alan@sanbi.ac.za

  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 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

  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 substitution S O U T H A F R I C A S O U T H - - R I K A N gaps

  11. End-to-end Not aligned

  12. Why do we want to compare sequences??

  13. Why do we want to compare sequences?? What is underlying hypothesis when you predict a function by comparing two sequences ?????

  14. Why do we want to compare sequences??

  15. Why do we want to compare sequences?? Positions not critical to function can mutate randomly!!!!!

  16. Why do we want to compare sequences?? Find an example where the above is not necessarily true

  17. Sequence Comparisons • Homology • similarity due to a common ancestor • no degrees of homology

  18. Sequence Comparisons

  19. Sequence Comparisons

  20. Sequence Comparisons

  21. Sequence Comparisons

  22. Sequence Comparisons Dot-plots

  23. Dot - plots

  24. Dot - plots

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

  26. Scoring Path

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