Safe Haskell | Safe-Inferred |
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Implement alignments/edit distance with affine gap penalties

I've seen g = (-10,-1) as the suggested price to pay for a gaps using BLOSUM62. Good choice as any, I guess.

- local_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a
- local_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList)
- global_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a
- global_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList)

# Smith-Waterman, or locally optimal alignment with affine gaps

local_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> aSource

Calculate local edit distance (Smith-Waterman alignment score)

local_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList)Source

Calculate local alignmnet (Smith-Waterman)