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Bio.Alignment.QAlign

Contents

Smith-Waterman
Needleman-Wunsch
Overlapping alignment.
Matrix construction
Interactive testing of alignments

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.

See also http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn052v1.

Synopsis

local_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double
local_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList)
global_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double
global_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList)
overlap_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double
overlap_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList)
qualMx :: Qual -> Qual -> (Chr, Chr) -> Double
test :: IO ()

Smith-Waterman
Locally optimal alignment with affine gaps, i.e. best infix match.

local_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double | Source

Calculate local edit distance (Smith-Waterman alignment score)

local_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList) | Source

Calculate local alignment (Smith-Waterman) (can we replace uncurry max' with fst - a local alignment must always end on a subst, no?)
Needleman-Wunsch
Globally optimal alignment with affine gaps, the whole sequences are matched.

global_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double | Source

Calculate global edit distance (Needleman-Wunsch alignment score)

global_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList) | Source

Calculate global alignment (Needleman-Wunsch)
Overlapping alignment.
The suffix of one sequence matches a prefix of another.

overlap_score :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> Double | Source

Calucalte best overlap score, where gaps at the edges are free The starting point is like for local score (0 cost for initial indels), the result is the maximum anywhere in the last column or bottom row of the matrix.

overlap_align :: QualMx t Double -> (Double, Double) -> Sequence t -> Sequence t -> (Double, EditList) | Source

Calucalte best overlap score, where gaps at the edges are free The starting point is like for local score (0 cost for initial indels), the result is the maximum anywhere in the last column or bottom row of the matrix.
Matrix construction

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

Interactive testing of alignments

test :: IO () | Source

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