1. Bioinformatics: The pair-wise alignment problem
Srinivas Jakkidi
CS 487

2. Overview Pair-wise alignment revisited Dynamic programming algorithm
Parallel extension

3. Pair-wise alignment
Inexact matching: comparing two sequences while allowing for some mismatch.
Extent of mismatch depends on type of sequence (protein vs. nucleotide)
Try to minimize the number of substitutions, inserts and deletes to convert one sequence to the other

4. Pair-wise alignment (cont.)
Insertion, deletion are considered same function – indel
Each mutation has an associated penalty
Try to minimize penalty (distance)

5. Dynamic programming algorithm
Dynamic programming: build solution using previous solutions for smaller subsequences
Stores values corresponding to partial results in a similarity matrix
We are trying to align two sequences X and Y of lengths m and n respectively.

6. Dynamic programming algorithm
Similarity matrix SM is of size mxn
SMi,j = max(SMi, j-1+ gp,
SMi-1, j-1+ ss,
SMi-1, j+ gp, 0)
gp is the gap penalty and ss is the substitution score

7. gp = -2
ss = 1(match)/-1(mismatch)

8. Multithreaded parallel implementation
Based on the EARTH execution model
SU – Synchronization unit
EU – Execution unit

10. Results
Almost linear speedup for large sequences