computeTm {crosshybDetector}R Documentation

Computing of melting temperature

Description

Computes the melting temperature (Tm) using the basic formula:

Tm= (wA+xT) * 2 + (yG+zC) * 4

where w,x,y,z are the number of the bases A,T,G,C in the sequence, respectively (from Marmur,J., and Doty,P. (1962) J Mol Biol 5:109-118).

Usage

computeTm(seqs, plot = FALSE)

Arguments

seqs a vector of nucleotide sequences
plot if TRUE, plot the histogram of Tm

Value

A vector with the same lenght of 'seqs' with the computed Tm

Author(s)

Paolo Uva

References

Marmur,J., and Doty,P. (1962) J Mol Biol 5:109-118

Examples

# Create a vector of 1000 random sequences of 30bp
code <- c("a", "c", "g", "t")
sequences <- vector("character", 1000)
for (i in 1:1000){
  sequences[i] <- paste(sample(code,30,replace=TRUE), collapse="")
}

# Compute the Tm and plot the corresponding histogram
tm <- computeTm(sequences, plot=TRUE)
table(tm)

[Package crosshybDetector version 1.0.4 Index]