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1. Find an optimal local alignment between the following two sequences, with respect to the scoring scheme p(a,b) = 1 if a = b, p(a,b) = -1 if a ≠ b, and g = -2.atcgatcagtcagc
cgatcagcatgcatcgatatccagtcagtcaccgcgatgctcgatcgtacgatcgaccgatcg
Answer:
An optimal alignment has been found that scored 8 points:
atcga-tcagtcagc
|||.|-|||||||.|
cgatcagcatgcatcgatatccagtcagtcaccgcgatgctcgatcgtacgatcgaccgatcg
A spreadsheet used to compute this local alignment is attached. Notice that there are two optimal local alignments, one contained in the other. The second one can be obtained from the alignment shown above by removing the last two alignment columns.
© 2015 Joao Meidanis