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

Overview Pair-wise alignment revisited Dynamic programming algorithm Parallel extension

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

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

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.

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

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

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

Results Almost linear speedup for large sequences