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Dynamic Programming (DP)

Dynamic Programming (DP). Three Steps: Initialization Matrix fill (scoring) Traceback (alignment) Global Alignment: Needleman-Wunsch Local Alignment: Smith-Waterman. G A A T T C A G T T A (sequence #1) G G A T C G A (sequence #2). http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html.

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Dynamic Programming (DP)

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  1. Dynamic Programming (DP) • Three Steps: • Initialization • Matrix fill (scoring) • Traceback (alignment) • Global Alignment: Needleman-Wunsch • Local Alignment: Smith-Waterman

  2. G A A T T C A G T T A (sequence #1) • G G A T C G A (sequence #2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  3. DP (Initialization) • Create N+1 by M+1 Matrix • M = Seq1 length = 11 • N = Seq2 length = 7 • Assuming no gap opening penalty, 0’s fill the first row and column G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  4. DP (Scoring) Simple Scoring Scheme • Si,j = 1 (Match) • Si,j = 0 (Mismatch) • w = 0 (Gap) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  5. F(i-1, j-1) + s(xi, yi) F(i-1, j) - w F(i, j-1) - w F(i,j) = max F(i-1, j-1) F(i, j-1) s(xi, yi) - w F(i-1, j) F(i,j) - w DP (Scoring) Si,j = 1 (Match), Si,j = 0 (Mismatch), w = 0 (Gap) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  6. F(i-1, j-1) + s(xi, yi) F(i-1, j) - w F(i, j-1) - w F(i,j) = max F(i-1, j-1) F(i, j-1) s(xi, yi) - w F(i-1, j) F(i,j) - w DP (Scoring) Si,j = 1 (Match), Si,j = 0 (Mismatch), w = 0 (Gap) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  7. F(i-1, j-1) + s(xi, yi) F(i-1, j) - w F(i, j-1) - w F(i,j) = max F(i-1, j-1) F(i, j-1) s(xi, yi) - w F(i-1, j) F(i,j) - w DP (Scoring) Si,j = 1 (Match), Si,j = 0 (Mismatch), w = 0 (Gap) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  8. F(i-1, j-1) + s(xi, yi) F(i-1, j) - w F(i, j-1) - w F(i,j) = max F(i-1, j-1) F(i, j-1) s(xi, yi) - w F(i-1, j) F(i,j) - w DP (Scoring) Si,j = 1 (Match), Si,j = 0 (Mismatch), w = 0 (Gap) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  9. F(i-1, j-1) + s(xi, yi) F(i-1, j) - w F(i, j-1) - w F(i,j) = max F(i-1, j-1) F(i, j-1) s(xi, yi) - w F(i-1, j) F(i,j) - w DP (Scoring) Completed Matrix http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  10. DP (Traceback) G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  11. DP (Traceback) Seq1 A | Seq2 A G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  12. DP (Traceback) Seq1 T A | Seq2 _ A G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  13. DP (Traceback) Seq1 T T A | Seq2 _ _ A G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  14. DP (Traceback) Seq1 G A A T T C A G T T A | | | | | | Seq2 G G A _ T C _ G _ _ A G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  15. DP (Traceback) Alternative: Seq1 G _ A A T T C A G T T A | | | | | | Seq2 G G _ A _ T C _ G _ _ A G A A T T C A G T T A (Seq1) G G A T C G A (Seq2) http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

  16. Basic Local Alignment Search Tool (BLAST) Heuristic Method

  17. BLAST

  18. BLAST

  19. BLAST

  20. BLAST

  21. DNA vs DNA Protein vs Protein DNA vs Protein Protein vs DNA What can we search and compare?

  22. Reading Frames

  23. The best BLAST program

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