| Safe Haskell | Safe |
|---|---|
| Language | Haskell98 |
Bio.Alignment.AAlign
Contents
Description
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 -> a
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)
Calculate local alignmnet (Smith-Waterman)