| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Bio.Motif.Search
- findTFBS :: Monad m => Bkgd -> PWM -> DNA a -> Double -> Bool -> Source m Int
- findTFBS' :: Bkgd -> PWM -> DNA a -> Double -> Bool -> [Int]
- findTFBSSlow :: Monad m => Bkgd -> PWM -> DNA a -> Double -> Source m Int
- maxMatchSc :: Bkgd -> PWM -> DNA a -> Double
- data SpaceDistribution = SpaceDistribution {}
- 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
Arguments
| :: Monad m | |
| => Bkgd | |
| -> PWM | |
| -> DNA a | |
| -> Double | |
| -> Bool | whether to skip ambiguous sequences. Recommend: True in most cases |
| -> Source m Int |
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
maxMatchSc :: Bkgd -> PWM -> DNA a -> Double Source #
the largest possible match scores starting from every position of a DNA sequence