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Biocomputation : Comparative Genomics

Biocomputation : Comparative Genomics. Tanya Talkar Lolly Kruse Colleen O’Rourke. DNA . Junk DNA. Conserved DNA. What is Biocomputation ?. Four Main Parts. Biomolecular computation Biological Computation Computational Biology Bioinformatics. Bioinformatics: . Sequence Analysis.

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Biocomputation : Comparative Genomics

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  1. Biocomputation: Comparative Genomics Tanya Talkar Lolly Kruse Colleen O’Rourke

  2. DNA

  3. Junk DNA Conserved DNA

  4. What is Biocomputation?

  5. Four Main Parts • Biomolecular computation • Biological Computation • Computational Biology • Bioinformatics

  6. Bioinformatics:

  7. Sequence Analysis • Very Functional! • Compare DNA between Species • Small Fragments • Return full sequence

  8. Computational Genomics • Needleman – Wunsch • Not used much • More Mapped Genomes = Computational Genomics!

  9. Alignment

  10. Global Alignment:Needleman - Wunsch • O(N3) • Fewest edit operations • Similar strings

  11. Local AlignmentSmith - Waterman • O(N2) • Dissimilar strings • Find high similarity regions

  12. Comparison

  13. B C A X A S X B A C S A

  14. Score 2 2 -1 2 -1 2 2

  15. Advantages:Global Alignment

  16. Advantages:Local Alignment

  17. BLAST • Basic Local Alignment Search Tool • FASTA

  18. Improvements • Increased Speed • Locate initial alignment hot spots • Statistical significance

  19. Terminology • Segment Pairs • Locally maximal segment pairs • Maximal segment pairs

  20. How it works • Query sentence, P • Database • Must have score over C! • Multiple segment pairs combined

  21. How it works • Extends each hit • Done efficiently • Truncates • Doesn’t find all pairs

  22. Proteins • Fixed length,W • Words above threshold • Each hit extended

  23. DNA • Word List • Exact matches • NOT dynamic programming

  24. Scoring • Blosum62 Matrix • Match (+2), Mismatch (-3), Gaps penalized

  25. Substitution Matrix • Represents Scoring Functions

  26. Multiple Sequence Alignment

  27. Methods of MSA • Progressive Alignment Construction • Iterative Methods • Hidden Markov Models • Genetic Algorithms and Simulated Annealing

  28. Comparative Genomics • Compare Species • Find Evolutionary Significances! • Low Level • High Level • Importance of Non Coding DNA

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