Bio.Motif.Alignment

Documentation

alignment :: AlignFn

alignmentBy

Arguments

:: DistanceFn

compute the distance between two aligned pwms

-> PenalFn

gap penalty

-> CombineFn

-> AlignFn

linPenal :: Double -> PenalFn

linear penalty

quadPenal :: Double -> PenalFn

quadratic penalty

cubPenal :: Double -> PenalFn

cubic penalty

expPenal :: Double -> PenalFn

exponentail penalty

l1 :: CombineFn

l2 :: CombineFn

l3 :: CombineFn

lInf :: CombineFn

type AlignFn

Arguments

 = PWM

-> PWM

-> (Double, (Bool, Int))

(distance, (on same direction, position w.r.t. the first pwm))

type CombineFn = Vector Double -> Double

combine distances from different positions of alignment