BCB 567/CprE 548 Fall 2007 Homework 5 Due Tuesday, Dec 4 Note: Use constant gap penalty and the following parameters, unless otherwise speciﬁed α denotes the score of a match, β denotes mismatch penalty, and γ denotes the gap penalty. 1. (4 points) Let s 1 ,s 2 ,...,s k be k sequences, each of length n . What is the maximum possible SP-score of a multiple sequence alignment between them? What is the worst possible SP-score? 2. (4 points) Devise an example of three (short) sequences s 1 , s 2 and s 3 such that the induced alignment of s 1 and s 2 has a lower score than the optimal pairwise alignment of s 1 and s 2 . 3. (5 points) Consider generalizing the k-band algorithm for the multiple sequence alignment of r sequences, of length n each. Derive a stopping condition for the same. 4. (5 points) In the center star method, the multiple alignment is constructed by successively aligning each new string to the center string s c . The order in which the strings are aligned to s c is not speciﬁed. Argue that the same multiple alignment is built, regardless of the
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