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Bio.Alignment.AAlign

Contents

Smith-Waterman, or locally optimal alignment with affine gaps
Needleman-Wunsch, or globally optimal alignment with affine gaps

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.
Synopsis

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 | Source

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)
Needleman-Wunsch, or globally optimal alignment with affine gaps

global_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a | Source

Calculate global edit distance (Needleman-Wunsch alignment score)

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

Calculate global alignment (Needleman-Wunsch)
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