ns.dg.self.hybridization: dG self-hybridization

In UvA-MAD/SeqLibR: Sequence Library

Description

Calculate the self-hybridization dG for a vector of sequences at a given temerature, using hybrid-ss-min from Unafold package.

Usage

ns.dg.self.hybridization(s, t = 75, c.Na = 1, c.Mg = 0,acid.type=c("DNA","RNA"))

Arguments

s	a vector of sequences in standard IUB/IUPAC nucleic acid codes
t	the temperature at which dG is calculated
c.Na	Natrium concentration at which dG is calculated
c.Mg	Magnesium concentration at which dG is calculated
acid.type	Calculate dG for DNA or RNA

Details

Currently only sequences containing determined nucleotides (ACGT) will produce output.

Value

A vector of reals giving the dG for all entered sequences

Note

The calculation is performed by calling the external program hybrid-ss-min. This program is part of the UNAFold nucleic acid folding package by Michael Zuker and Nick Markham. This package must be installed to in order to use the function.

Author(s)

Wim de Leeuw

Examples

  ns.dg.self.hybridization(c("ATATATATA","CCCCGGGCGCG","CGCGGGGCATTATATCTACTACTAGTATCT"));

UvA-MAD/SeqLibR documentation built on May 9, 2019, 9:40 p.m.