calcTm {HELP} | R Documentation

## Calculate Tm

### Description

Calculate melting temperature (Tm) using the nearest-neighbor base-stacking algorithm and the unified thermodynamic parameters.

### Usage

    calcTm(x, ...)

### Arguments

`x` | characters containing nucleotide sequences (ex: "ATCGGAA") or an object of class `ExpressionSet`
`...` | Additional arguments passed to methods: `\item{strand1.concentration}`{ numeric value specifying concentration of strand 1 (default is 2e-07)} `\item{strand2.concentration}`{ numeric value specifying concentration of strand 2 (default is 2e-07)} `\item{method}`{ character value specifying the Tm algorithm to use (default is "nearest-neighbor"); currently not supported }

### Value

Returns a numerical value indicating the predicted melting temperature (Tm) of the sequence in degrees Celsius. A value of NA is returned if the function encounters an error that prevents proper Tm calculation.

### Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu)

### References

Allawi, H.T. and SantaLucia, J., Jr. (1997) Thermodynamics and NMR of internal G.T mismatches in DNA, Biochemistry, 36, 10581-10594.

### See Also

`calcTm-methods`, `base.stacking.thermodynamics`, `calcGC`

### Examples

    #demo(pipeline,package="HELP")

    calcTm("GTGTGGCTACAGGTGGGCCGTGGCGCACCTAAGTGAGGACAGAGAACAAC")
    calcTm("GTGTGGCTACAGGTGGGCCGTGGCGCACCTAAGTGAGGACAGAGAACAAC",strand1.concentration=1E-5,strand2.concentration=2E-8)

[Package HELP version 1.0.0 Index]