Safe Haskell	None
Language	Haskell2010

Bio.Motif.Search

Synopsis

findTFBS :: Monad m => Bkgd -> PWM -> DNA a -> Double -> Bool -> ConduitT i Int m ()
findTFBS' :: Bkgd -> PWM -> DNA a -> Double -> Bool -> [Int]
findTFBSSlow :: Monad m => Bkgd -> PWM -> DNA a -> Double -> ConduitT i Int m ()
maxMatchSc :: Bkgd -> PWM -> DNA a -> Double
data SpaceDistribution = SpaceDistribution {
- _motif1 :: Motif
- _nSites1 :: (Int, Int)
- _motif2 :: Motif
- _nSites2 :: (Int, Int)
- _same :: [(Int, Int)]
- _opposite :: [(Int, Int)]
}
spaceConstraint :: [(Motif, Motif)] -> Bkgd -> Double -> Int -> Int -> DNA a -> [SpaceDistribution]
spaceConstraintHelper :: (Vector Int, Vector Int) -> (Vector Int, Vector Int) -> Int -> Int -> ([(Int, Int)], [(Int, Int)])

Documentation

findTFBS Source #

Arguments

:: 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

data SpaceDistribution Source #

Constructors

SpaceDistribution
Fields _motif1 :: Motif _nSites1 :: (Int, Int) _motif2 :: Motif _nSites2 :: (Int, Int) _same :: [(Int, Int)] _opposite :: [(Int, Int)]

Instances

Read SpaceDistribution Source #
Instance details Defined in Bio.Motif.Search Methods readsPrec :: Int -> ReadS SpaceDistribution # readList :: ReadS [SpaceDistribution] # readPrec :: ReadPrec SpaceDistribution # readListPrec :: ReadPrec [SpaceDistribution] #
Show SpaceDistribution Source #
Instance details Defined in Bio.Motif.Search Methods showsPrec :: Int -> SpaceDistribution -> ShowS # show :: SpaceDistribution -> String # showList :: [SpaceDistribution] -> ShowS #

spaceConstraint Source #

Arguments

:: [(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

spaceConstraintHelper :: (Vector Int, Vector Int) -> (Vector Int, Vector Int) -> Int -> Int -> ([(Int, Int)], [(Int, Int)]) Source #