alignment

# 2 n n n k0 mn nm k k n towards a dynamic programming

This preview shows page 1. Sign up to view the full content.

This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: tches – (#mismatches) μ – (#indels) σ •  Objective: ﬁnd the best scoring alignment Number of pairwise alignments •  For two sequences of length n: ￿ 2n n ￿ (2n)! 22 n = ≈√ 2 (n!) πn •  Derived using Stirling’s approximation: n! ≈ √ 2π n ￿ n ￿n k=0 ￿￿ ￿ ￿ ￿ mn n+m = k k n Towards a dynamic programming algorithm for pairwise alignment •  •  •  •  •  The Change Problem The Manhattan Tourist Problem The Longest Common Subsequence Problem Edit Distance Sequence Alignment e 2 A greedy algorithm for Change The Change Problem Goal: Convert some amount of money M into g iven denominations, using the fewest possible number of coins Input: An amount of money M, and an array of d denominations c = (c1, c2, …, cd), in decreasing order of value (c1 > c2 > … > cd) Output: A list of d integers i1, i2, …, id s.t. c1i1 + c2i2 + … + cdid = M and i1 + i2 + … + id is minimal •  Use the maximal number of the largest denomination •  Fails: example - change 40 when we have denominatio...
View Full Document

## This note was uploaded on 02/10/2014 for the course CS 548 taught by Professor Asaben-hur during the Spring '12 term at Colorado State.

Ask a homework question - tutors are online