1. CS502: Algorithms in Computational Biology
Sequence Alignment
Tanya Berger-Wolf
CS502: Algorithms in Computational Biology
February 2, 2016

2. Comparing Genes in Two Genomes
Small islands of similarity corresponding to similarities between exons
Such comparisons are quite common in biology research

3. String Similarity ocurrance occurrence How similar are two strings? o- o c c u r r e n c e
6 mismatches, 1 gap o c - u r r a n c e o c c u r r e n c e
1 mismatch, 1 gap o c - u r r - a n c e o c c u r r e - n c e
0 mismatches, 3 gaps

4. Edit Distance Applications. Basis for Unix diff. Speech recognition.
Computational biology.
Edit distance. [Levenshtein 1966, Needleman-Wunsch 1970]
Gap penalty ; mismatch penalty pq.
Cost = sum of gap and mismatch penalties. C T G A C C T A C C T - C T G A C C T A C C T
Levenshtein introduced concept of edit-distance; Needleman-Wunsch first applied it to aligning biological sequences; our algorithm is closest in spirit to Smith-Waterman (but their algorithm is for local alignment)
Presumably alpha_pp = 0, but assumption not needed (could be a profit instead of penalty)
bonus application: spam filter - compare message with known spam messages C C T G A C T A C A T C C T G A C - T A C A T
TC + GT + AG+ 2CA
2 + CA

5. Sequence Alignment
Goal: Given two strings X = x1 x xm and Y = y1 y yn find alignment of minimum cost.
Def. An alignment M is a set of ordered pairs xi-yj such that each item occurs in at most one pair and no crossings.
Def. The pair xi-yj and xi'-yj' cross if i < i', but j > j'.
Ex: CTACCG vs. TACATG. Sol: M = x2-y1, x3-y2, x4-y3, x5-y4, x6-y6. x1 x2 x3 x4 x5 x6 C T A C C - G - T A C A T G y1 y2 y3 y4 y5 y6

6. Dynamic Programming History
Bellman. Pioneered the systematic study of dynamic programming in the 1950s.
Etymology.
Dynamic programming = planning over time.
Secretary of Defense was hostile to mathematical research.
Bellman sought an impressive name to avoid confrontation.
"it's impossible to use dynamic in a pejorative sense"
"something not even a Congressman could object to"
Reference: Bellman, R. E. Eye of the Hurricane, An Autobiography.

7. Dynamic Programming Applications
Areas.
Bioinformatics.
Control theory.
Information theory.
Operations research.
Computer science: theory, graphics, AI, systems, ….
Some famous dynamic programming algorithms.
Viterbi for hidden Markov models.
Unix diff for comparing two files.
Smith-Waterman for sequence alignment.
Bellman-Ford for shortest path routing in networks.
Cocke-Kasami-Younger for parsing context free grammars.

8. Sequence Alignment: Problem Structure
Def. OPT(i, j) = min cost of aligning strings x1 x xi and y1 y yj.
Case 1: OPT matches xi-yj.
pay mismatch for xi-yj + min cost of aligning two strings x1 x xi-1 and y1 y yj-1
Case 2a: OPT leaves xi unmatched.
pay gap for xi and min cost of aligning x1 x xi-1 and y1 y yj
Case 2b: OPT leaves yj unmatched.
pay gap for yj and min cost of aligning x1 x xi and y1 y yj-1

9. Sequence Alignment: Algorithm
Analysis. (mn) time and space.
English words or sentences: m, n  10.
Computational biology: m = n = 100, billions ops OK, but 10GB array?
Sequence-Alignment(m, n, x1x2...xm, y1y2...yn, , ) {
for i = 0 to m
M[0, i] = i
for j = 0 to n
M[j, 0] = j
for i = 1 to m
for j = 1 to n
M[i, j] = min([xi, yj] + M[i-1, j-1],
 + M[i-1, j],
 + M[i, j-1])
return M[m, n] }

10. Sequence Alignment: Algorithmy
n + 1  T A C 2 3 4 1 5 G 6
Gap penalty =
Mismatch penalty = 1 x
m + 1 C T A - G y1 y2 y3 y4 y5 y6 x2 x3 x4 x5 x1 x6

11. 6.7 Sequence Alignment in Linear Space
1-24,26-37

12. Sequence Alignment: Linear Space
Q. Can we avoid using quadratic space?
Easy. Optimal value in O(m + n) space and O(mn) time.
Compute OPT(i, •) from OPT(i-1, •).
No longer a simple way to recover alignment itself.
Theorem. [Hirschberg 1975] Optimal alignment in O(m + n) space and O(mn) time.
Clever combination of divide-and-conquer and dynamic programming.
Inspired by idea of Savitch from complexity theory.

13. Sequence Alignment: Linear Space
Edit distance graph.
Let f(i, j) be shortest path from (0,0) to (i, j).
Observation: f(i, j) = OPT(i, j).  y1 y2 y3 y4 y5 y6 
0-0 x1
edit distanace graph would take (mn) space to write down   x2
i-j x3
m-n

14. Sequence Alignment: Linear Space
Edit distance graph.
Let f(i, j) be shortest path from (0,0) to (i, j).
Can compute f (•, j) for any j in O(mn) time and O(m + n) space. j  y1 y2 y3 y4 y5 y6 
0-0 x1
edit distanace graph would take (mn) space to write down x2
i-j x3
m-n

15. Sequence Alignment: Linear Space
Edit distance graph.
Let g(i, j) be shortest path from (i, j) to (m, n).
Can compute by reversing the edge orientations and inverting the roles of (0, 0) and (m, n)  y1 y2 y3 y4 y5 y6 
0-0  x1
i-j  x2 x3
m-n

16. Sequence Alignment: Linear Space
Edit distance graph.
Let g(i, j) be shortest path from (i, j) to (m, n).
Can compute g(•, j) for any j in O(mn) time and O(m + n) space. j  y1 y2 y3 y4 y5 y6 
0-0 x1
i-j x2 x3
m-n

17. Sequence Alignment: Linear Space
Observation 1. The cost of the shortest path that uses (i, j) is f(i, j) + g(i, j).  y1 y2 y3 y4 y5 y6 
0-0 x1
i-j x2 x3
m-n

18. Sequence Alignment: Linear Space
Observation 2. let q be an index that minimizes f(q, n/2) + g(q, n/2). Then, the shortest path from (0, 0) to (m, n) uses (q, n/2).
n / 2  y1 y2 y3 y4 y5 y6 
0-0 x1
i-j q x2 x3
m-n

19. Sequence Alignment: Linear Space
Divide: find index q that minimizes f(q, n/2) + g(q, n/2) using DP.
Align xq and yn/2.
Conquer: recursively compute optimal alignment in each piece.
n / 2  y1 y2 y3 y4 y5 y6 
0-0 x1
i-j q x2 x3
m-n

20. Sequence Alignment: Running Time Analysis Warmup
Theorem. Let T(m, n) = max running time of algorithm on strings of length at most m and n. T(m, n) = O(mn log n).
Remark. Analysis is not tight because two sub-problems are of size (q, n/2) and (m - q, n/2). In next slide, we save log n factor.

21. Sequence Alignment: Running Time Analysis
Theorem. Let T(m, n) = max running time of algorithm on strings of length m and n. T(m, n) = O(mn).
Pf. (by induction on n)
O(mn) time to compute f( •, n/2) and g ( •, n/2) and find index q.
T(q, n/2) + T(m - q, n/2) time for two recursive calls.
Choose constant c so that:
Base cases: m = 2 or n = 2.
Inductive hypothesis: T(m, n)  2cmn.