bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Inferred

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

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)

# 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

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)

Calculate global alignment (Needleman-Wunsch)