calc.dh.ds: Calculate changes in enthalpy and entropy of oligonucleotides...

In Santaris/affinity: Functions to do thermodynamics on oligonucleotides

Description

For an input character vector of oligonucleotide sequences, and an optional input character vector of RNA target sequences, this function calculates/predicts enthalpy (dh) and entropy (ds), based on a nearest-neigbhbor model.

Usage

calc.dh.ds(oligos, targets = NULL, parameters.in = NULL, parallel=F, cores=NA)

Arguments

oligos	A character vector of oligonucleotide sequences in camel-case (uppercase: LNA, lowercase: DNA) in the 5' to 3' direction.
targets	A character vector of RNA target sequences in the 3' to 5' direction (opposite of normal direction). If NULL (standard) all target sequences are assumed to be perfectly complementary to their respective oligonucleotides.
parameters.in	A dataframe with nearest neighbor parameters for all possible dinucleotides. When NULL (standard), the dataframe thermopar is used, which is part of the package.
parallel	logical(T/F), should the computation be parallelized.
cores	integer, the number of cores used for parallel computation. If NA, use the maximal number of cores. This parameter is only relevant if parallel=T.

Details

See calculate.affinity for details.

Value

Returns a dataframe with one row for each oligonucleotide, and 2 columnns:

dh	The enthalpy (cal/mol).
ds	The entropy (cal/(mol*K)).

Author(s)

Peter Hagedorn and Morten Lindow

Examples

calc.dh.ds(rep("AAAgtacaaTTG",10))

Santaris/affinity documentation built on May 9, 2019, 12:43 p.m.