| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
BioInf.ViennaRNA.Bindings
Contents
Description
Bindings to important functions in the ViennaRNA library.
TODO Anything here that is not thread-safe should internally use a mutex!
- mfe :: String -> IO (Double, String)
- mfeTemp :: Double -> String -> IO (Double, String)
- circmfe :: String -> IO (Double, String)
- eos :: String -> String -> IO Double
- eosTemp :: Double -> String -> String -> IO Double
- eosCirc :: String -> String -> IO Double
- part :: String -> IO (Double, String, Array (Int, Int) Double)
- partConstrained :: String -> String -> IO (Double, String, Array (Int, Int) Double)
- circPart :: String -> IO (Double, String, Array (Int, Int) Double)
- circPartConstrained :: String -> String -> IO (Double, String, Array (Int, Int) Double)
- centroidTemp :: Double -> String -> IO (Double, String)
- coeos :: String -> String -> Int -> IO Double
- comfe :: String -> Int -> IO (Double, String)
- copart :: String -> Int -> IO (CofoldF, String, Array (Int, Int) Double)
- copartConstrained :: String -> String -> Int -> IO (CofoldF, String, Array (Int, Int) Double)
- duplexFold :: String -> String -> IO Duplex
- data CofoldF = CofoldF {}
- data Duplex = Duplex {}
Documentation
mfe :: String -> IO (Double, String) Source #
Fold a sequence into an optimal secondary structure. Returns a pair of energy and structure.
eos :: String -> String -> IO Double Source #
Given a sequence and a structure, returns the energy of the sequence/structure pair.
part :: String -> IO (Double, String, Array (Int, Int) Double) Source #
Given a string, calculates the partition function for said string. Returns the ensemble energy, a string with where each nucleotide position is annotated with the strength of the potential pairing, and the whole base pair probability table.
RNAcofold
copart :: String -> Int -> IO (CofoldF, String, Array (Int, Int) Double) Source #
Cofolded partition function. Makes the set of different partfun values from cofoldF available.
copartConstrained :: String -> String -> Int -> IO (CofoldF, String, Array (Int, Int) Double) Source #
Constructors
| CofoldF | |
Constructors
| Duplex | |