bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Infered

Bio.Alignment.SAlign

Contents

- Smith-Waterman, or locally optimal alignment
- Needleman-Wunsch, or globally optimal alignment

Description

Simple alignment of sequences

Standard alignment/edit distance

Synopsis

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

# Smith-Waterman, or locally optimal alignment

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

# Needleman-Wunsch, or globally optimal alignment

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

Calculate alignments.