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Assignment 2

# Assignment 2 - Introduction to Bioinformatics/Elements of...

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Introduction to Bioinformatics/Elements of Bioinformatics Assignment 2 Due: April 14, 2009 Submit in class or via email to [email protected] 1. Determine the optimal global alignment(s) between CDAA and AEECA by the dynamic programming method. Use the following scoring matrix and a linear gap penalty of 2. Penalize gaps at the ends of the sequences. A C D E A 2 -2 -2 -1 C -2 1 0 0 D -2 0 2 -2 E -1 0 -2 2 Fill in the rest of the dynamic programming table (10%) and determine the optimal alignment(s) between CDAA and AEECA (5%). 1 2 3 4 5 A E E C A 0 -2 -4 -6 -8 -10 1 C -2 2 D -4 3 A -6 4 A -8 Repeat the dynamic programming procedure using an affine gap penalty scheme w = 1.8 + 0.4x where x is the length of gap. Fill in the rest of the dynamic programming table (5%) and determine the optimal alignment(s) (2%). 1 2 3 4 5 A E E C A 0.0 -2.2 -2.6 -3.0 -3.4 -3.8 1 C -2.2 -2.0 -2.2 -2.6 -2.0 -4.2 2 D -2.6 -4.2 -4.0 -4.2 -2.6 -4.0 3 A -3.0 -0.6 -2.8 -3.2 4 A -3.4 -1.0 -1.6

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2. Consider the following block of aligned sequences: LIAVL LIAVI LAAII AVLLI Construct a BLOSUM matrix from the alignment block, assume no clustering of sequences. Consider only the interconversions among L, I, A and V. (10%)
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Assignment 2 - Introduction to Bioinformatics/Elements of...

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