Sequence Comparison.pdf

70 4 Homology Search Tools
BLOSUM substitution matrix is often employed, whereas for DNA sequences, an
identity is given a positive score and a mismatch is penalized by a negative score.
Figure 4.5 depicts the similarity scores of all the pairs of the residues of the two
sequences GATCCATCTT and CTATCATTCTG, where an identity is given a score
+5 and a mismatch is penalized by -4.
Let a sequence segment be a contiguous stretch of residues of a sequence. The
score for the aligned segments a i a i+1 ...a i+l−1 and b j b j+1 ...b j+l−1 of length l is
the sum of the similarity scores for each pair of aligned residues (a i+k ,b j+k ) where
0 ≤ k