Bio.Motif.Search

Documentation

findTFBS

Arguments

:: Monad m

=> Bkgd

-> PWM

-> DNA a

-> Double

-> Bool

whether to skip ambiguous sequences. Recommend: True in most cases

-> ConduitT i (Int, Double) m ()

given a user defined threshold, look for TF binding sites on a DNA sequence, using look ahead search. This function doesn't search for binding sites on the reverse strand

findTFBSWith

Arguments

:: Monad m

=> Vector Double

best possible match score of suffixes

-> Bkgd

-> PWM

-> DNA a

-> Double

-> Bool

whether to skip ambiguous sequences. Recommend: True in most cases

-> ConduitT i (Int, Double) m ()

findTFBSSlow :: Monad m => Bkgd -> PWM -> DNA a -> Double -> ConduitT i (Int, Double) m ()

use naive search

maxMatchSc :: Bkgd -> PWM -> DNA a -> Double

the largest possible match scores starting from every position of a DNA sequence

optimalScoresSuffix :: Bkgd -> PWM -> Vector Double