HELP (version 1.30.0)

calcTm: 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:

strand1.concentration

numeric value specifying concentration of strand 1 (default is 2e-07)

strand2.concentration

numeric value specifying concentration of strand 2 (default is 2e-07)

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.

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)