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hw5Solutions

# hw5Solutions - BCB 567/CprE 548 Fall 2007 Homework 5...

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Unformatted text preview: BCB 567/CprE 548 Fall 2007 Homework 5 Solutions 1. The maximum possible SP score occurs when all sequences are the same. In this case the total score is n k 2 α . This is because each column is perfectly matched: AAAA AAAA .... AAAA The worst possible SP score occurs when each string consists of a single unique character from Σ. In this case, the SP score becomes one of two equations. If all sequences are aligning (for a MSA length of n ), the score is: n k 2 ! β = nk ( k- 1) β 2 AAAA BBBB .... KKKK If all sequences are aligned with gaps (total MSA lenght of nk ), the score is: nk ( k- 1) γ = nk ( k- 1)2 γ 2 = n k 2 ! 2 γ AAAA----...--------BBBB...---- ...--------...KKKK Either of these cases could have lower total score depending on whether or not β < 2 γ . 1 2. Example: XYX, YXY, and YXX. α = 1 , γ =- 2 , β =- 1 In this case, the multiple alignment: XYX YXY YXX is optimal with score of -3. However, obviously the pairwise aligment XYX YXY with a score of -3 is not optimal. XYX--YXY with a score of -2 is optimal. 2 3. The first thing we should do is generalize the k-band to d dimensions. Recall that we defined the k-band to be all cells such that | i- j |...
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hw5Solutions - BCB 567/CprE 548 Fall 2007 Homework 5...

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