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423f11-hw1

# 423f11-hw1 - CMSC 423 Homework#1 Due Sep 22 at the start of...

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CMSC 423 Homework #1: Due: Sep. 22 at the start of class You may discuss these problems with your classmates, but you must write up your solutions inde- pendently , without using common notes or worksheets. You must indicate at the top of your homework who you worked with. Your write up should be clear, concise, and neat. You are trying to convince a skeptical reader that your answers are correct. Messy or hard-to-read homeworks will not be graded. 1. Consider the strings a = “nonsense” and b = “oneness”. Suppose that a gap costs 5, a match cost - 1, and the cost of aligning two mismatching characters x and y is given by the function cost : cost(n,o) = cost(n,s) = cost(n,e) = 2 cost(o,e) = cost(o,s) = cost(s,e) = 1 (a) Provide a well-labeled dynamic programming table for the global alignment between a and b . Show backtracking arrows. Find the optimal, lowest-cost alignment and its cost. (b) Provide a well-labeled dynamic programming table for the local alignment between a and b . Show backtracking arrows. Find the optimal alignment and its cost.
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