| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
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)
Produced by Haddock version 2.4.2