bioinformatics-toolkit-0.5.0: A collection of bioinformatics tools

Safe HaskellNone




findTFBS Source #


:: Monad m 
=> Bkgd 
-> PWM 
-> DNA a 
-> Double 
-> Bool

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

-> ConduitT i Int 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

findTFBS' :: Bkgd -> PWM -> DNA a -> Double -> Bool -> [Int] Source #

a parallel version of findTFBS

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

use naive search

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

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

spaceConstraint Source #


:: [(Motif, Motif)]

motifs, names must be unique

-> Bkgd

backgroud nucleotide distribution

-> Double

p-Value for motif finding

-> Int

half window size, typical 5

-> Int

max distance to search, typical 300

-> DNA a 
-> [SpaceDistribution] 

search for spacing constraint between two TFs