Introduction to Sequence Alignment. Why Align Sequences?. Find homology within the same species Find clues to gene function Practical issues in experiments Find homology in other species Gather info for an evolutionary model Gene families. The Most Visual Way of Aligning Two Sequences.
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Gibbs & McIntyre
A possible alignment:
There are many possible alignments
For example, compare:
Which one is better?
(# matches) – (# mismatches) – (# gaps) x 2
Score: (+1x13) + (-1x2) + (-2x4) = 3
Score: (+1x5) + (-1x6) + (-2x11) = -23
Consider the best alignment score of two sequences s, t at base/residue i+1, j+1, respectively:
– A G C –
– A A A C –
We fill the matrix using the recurrence rule
d(AAAC,AGC) = -1
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
J. Mol. Biol. 48: 443-453
“Identification of Common Molecular Subsequences”
J. Mol. Biol., 147:195-197
The best score or start over
Best aligned subsequences