Pairwise alignment with scoring on tuples
Pairwise alignment of two sequences a, b usually assumes a and b being sequences over the same alphabet A and a scoring function s: A×A→ℝ operating on symbol pairs. The framework presented here extends this to a scoring function s: A p ×B q →ℝ operating on p-tuples and q-tuples of symbols, where the scoring tuples can have an arbitrary (but not complete) overlap.
We show that, if the alphabets A and B are finite and p and q are constant, the resulting algorithms have the same asymptotic time and space complexity as their single symbol counterparts.
This framework has been applied successfully to the codon-wise alignment of prokaryotic and eukaryotic genes.
KeywordsSpace Complexity Dynamic Programming Algorithm Pairwise Alignment Good Alignment Global Alignment
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