Bio.Alignment.QAlign

Contents

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

Description

Quality-aware alignments

Generally, quality data are ignored for alignment/pattern searching like Smith-Waterman, Needleman-Wunsch, or BLAST(p|n|x). I believe that accounting for quality will at the very least affect things like BLAST statistics, and e.g. is crucial for good EST annotation using Blastx.

This module performs sequences alignments, takes quality values into account.

Synopsis

local_score :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> Double

local_align :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> (Double, EditList)

global_score :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> Double

global_align :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> (Double, EditList)

qualMx :: Qual -> Qual -> (Chr, Chr) -> Double

Smith-Waterman, or locally optimal alignment with affine gaps

local_score :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> Double

Source

Calculate local edit distance (Smith-Waterman alignment score)

local_align :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> (Double, EditList)

Source

Calculate local alignmnet (Smith-Waterman)

Needleman-Wunsch, or globally optimal alignment with affine gaps

global_score :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> Double

Source

Calculate global edit distance (Needleman-Wunsch alignment score)

global_align :: QualMx Double -> (Double, Double) -> Sequence -> Sequence -> (Double, EditList)

Source

Calculate global alignment (Needleman-Wunsch)

Matrix construction

qualMx :: Qual -> Qual -> (Chr, Chr) -> Double

Source

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