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Today’s Agenda

Today’s Agenda. Exam post-mortem (15-25 min) Grades & Status (5 min) Derek’s presentation (15-25 min) Exam #2: Question #1 (time permitting). Exam post-mortem. 1. Edit distance -3 if you made a minor (cascading) error -3 if you mis-initialized the matrix

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Today’s Agenda

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  1. Today’s Agenda • Exam post-mortem (15-25 min) • Grades & Status (5 min) • Derek’s presentation (15-25 min) • Exam #2: Question #1 (time permitting)

  2. Exam post-mortem 1. Edit distance • -3 if you made a minor (cascading) error • -3 if you mis-initialized the matrix • For the Final: Check your answer by hand. • And Remember…

  3. Exam post-mortem 2. Naïve Approach • No approach can ever produce a solution that is better than optimal. • No edit distance can be smaller than the optimal edit distance. • Full credit given if noticed that matching first A led to a sub-optimal answer

  4. Exam post-mortem 4. bits, binary code, 1’s and 0’s, etc 5. Deoxyribonucleic Acid 6. RNA  Uracil, Guanine, Cytosine, Adenine 8. A gene is segment of DNA that encodes a protein or regulates a gene that does.

  5. Acid Sugar Sugar Sugar Sugar Sugar Sugar Sugar Sugar A T G T A T A C Acid Acid Acid Acid Acid Acid Acid Exam post-mortem 9. Draw picture

  6. Exam post-mortem 10. 3 billion 11. Transcription  Translation 12. Intron regions are sliced out (removed) 13. In reality, there are 20 amino acids in protein sequences 14. In theory, 3 RNA bases can encode 43=64 different combinations4 different RNA bases ACGU

  7. Exam post-mortem 15. 40-50 Several times I mentioned that 10-20 was not accurate. 16. Several hundred. Technically 100’s but 1000’s is OK. 17. 3000

  8. Exam post-mortem 18. Global alignment -> Whole genome comparison 19. Local alignment -> Searching for genes 20. Multiple alignment -> Shared pattern discovery -> gene discovery

  9. Exam post-mortem 21. Finding the first two symbols that match requires: • Finding two symbols that match such that • The number of edits to match the two symbols is minimized Some times the best match is deep in the sequences Matching the pair of A’s is the best options (so far)

  10. Exam post-mortem 21. Finding the first two symbols that match : • Is as hard (computationally) as solving the whole problem. • What if there are no symbols that match • What if the sequences have 100’s or 1000’s of different types of symbols

  11. Exam post-mortem min = i+j; for (i = 0; i < n && i < min; i++) for (j = 0; j < n && j < min; j++) if ((seq1[i] == seq2[j]) &&((i+j) < min)) { min = i+j; mini = i; minj = j; } The first match occurs at seq1[mini] and seq2[minj].

  12. Today’s Agenda • Exam post-mortem (15-25 min) • Grades & Status (5 min) • Derek’s presentation (15-25 min) • Exam #2: Question #1 (time permitting)

  13. Grades & Status

  14. Grades & Status

  15. Grades & Status • Things will get harder • Right now, there is no work load… • Soon, project #2 will be out • The remaining material involves • Math (probability) • Algorithms • Code

  16. Grades & Status • Advice: • Get moving with your paper and presentation. Get it out of the way. • Project #2 will be challenging… • Project #2 will be given out on Tuesday.

  17. Today’s Agenda • Exam post-mortem (15-25 min) • Grades & Status (5 min) • Derek’s presentation (15-25 min) • Exam #2: Question #1 (time permitting)

  18. Today’s Agenda • Exam post-mortem (15-25 min) • Grades & Status (5 min) • Derek’s presentation (15-25 min) • Exam #2: Question #1 (time permitting)

  19. Exam #2: Question #1 • Given two sequences, compute the optimal local alignment.

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