BioInf.Params

RNA-folding parameter space.

TODO find better names for types, functions, and minima/maxima.

Documentation

data Params

A (very) rich set of paramters.

TODO 1xn interior loops should be tested (how often do they occur?)

TODO external loop

Constructors

Params

Fields

hairpinLength :: PaLength

hairpinClose :: PaExtPairNN

stem :: Pa2ExtPairs

stemTriplet :: Pa2ExtPairs

interiorLength :: PaLength

interiorAsym :: PaLength

interiorClose :: PaExtPairNN

bulgeLength :: PaLength

bulgeTriplet :: Pa2ExtPairs

bulgeClose :: PaExtPair

mbClose :: PaExtPairNN

multiBranched :: Double

multiHelix :: Double

multiUnpaired :: Double

pairDistance :: PaDistance

interMolInit :: Double

Instances

Read Params

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types

type PaLength = PrimArray Int Double

An array which encodes length information

type PaDistance = PrimArray Int Double

This is an experimental annotation for long-distance interactions

type PaExtPair = PrimArray ExtPair Double

An array holding information for one extended pair.

type Pa2ExtPairs = PrimArray (ExtPair, ExtPair) Double

An array holding information for two extended pairs, e.g. stems.

type PaExtPairNN = PrimArray (ExtPair, Nuc, Nuc) Double

An array holding information for one extended pair and two unpaired nucleotides, closes a loop.