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]