Biobase.Turner

Mathews / Turner nearest neighbor energy tables for interactions between RNA-RNA and DNA-DNA. Using lazy tables for easy filling of missing data. Transform tables into uvectors for efficient access.

Documentation

type TurnerTables = Turner2004 Basepair Nucleotide Double

Data structure containing all necessary tables for the Turner 2004 model. Note the temperature, using an additional function, rescaling becomes possible. A Show and a Read instance are automatically derived but one should use the Turner andor Vienna importexport facilities. All data uses complete tables, where any base can pair with any other. Missing data (. in tables) is given by Nothing, otherwise we have 'Just Int'.

In general, have a look here: url{http:rna.urmc.rochester.eduNNDBturner04/index.html} where parameters are explained.

Conversion from Turner to Vienna is only possible in one direction as a number of parameters are not used in Vienna RNA Folding.

type TurnerEntropy = TurnerTables

type TurnerEnthalpy = TurnerTables

type Temperature = Double

type TurnerSet = (Temperature, TurnerEntropy, TurnerEnthalpy)

type Basepair = (Nucleotide, Nucleotide)