How to Score Alignments
• “Better” depends on how we
want to assign scoring
values
• We need scoring values for
– Identical residues
– Gaps
– Residues in same group
• Polar
• Hydrophobic
• Charged
– Residues in different groups
• We simplify things for our
examples
– Allow all 26 letters, not just
the 20 that are used to
represent amino acids
– We assume 2 groups
• Vowels
• Consonants
– Scoring values
• 4 for identical
• 1 for same group
• 0 for different groups
• -1 for gap
CS409 - Spring 2000
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