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Module 6.4 · Topic 2
Module 6.4 · Topic 2
Not every mismatch between two sequences means the same thing
Two aligned protein sequences differ at one position — Leucine in one, Isoleucine in the other. Two completely different sequences also differ at exactly one position — Leucine versus Proline. Both are "one substitution." Treating them identically would throw away real biochemical information.
Leucine and Isoleucine are both hydrophobic amino acids of similar size and shape. Proline has a rigid ring structure that disrupts normal secondary structure formation. Should a Leucine-to-Isoleucine substitution and a Leucine-to-Proline substitution be scored identically in a sequence alignment?
A scoring matrix used in sequence alignment assigns different scores to different amino acid substitutions based on:
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