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# practicequestion - T is di³erent from the gap opening and...

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CMPT 341 (Introduction to Biocomputing) Homework Assignment 2, Fall 2004 Due date: Oct 18, 2004 1. Given two strings T and P from the DNA alphabet, an integer k , and a score matrix for aligning each character in the alphabet to the others you are asked to find the substring of T with length at least k and whose alignment score to P is maximum. Develop a dynamic programming solution to the problem. Write the algorithm in simple pseudocode and explain briefly how it works. Analyze its running time. (10 pts) 2. Generalize the Needleman-Wunsch global alignment algorithm on two sequences S and T with affine gap penalties, so that the gap opening and gap extension penalties for T
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Unformatted text preview: T is di³erent from the gap opening and gap extension penalties for S can be di³erent (thus the user needs to input the gap opening and gap extension scores for T and S separately). Write down the pseudocode of your algorithm and explain how it works. Analyze its running time. (10 pts) 3. Problem 31 in pp 247, GusFeld. (10 pts) 4. Problem 26 in pp 310, GusFeld (10 pts). (Read section 12.5 (pp 287-293) Frst.) 5. Problem 7 in pp 366, GusFeld (10 pts). 6. Problem 9 in pp 366, GusFeld (10 pts). (Read section 14.3 (pp 336-340) Frst.) 7. Problem 11 in pp 367, GusFeld (10 pts). (Read section 14.6 (pp 343-350) Frst.) 1...
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