MeltingTemperatureInterface
in
Interface MeltingTemperatureInterface
Tags
Table of Contents
Methods
- calculateGcPercent() : float
- calculateMaximumTm() : float
- The highest melting temperature a degenerate primer could have, resolving every ambiguous symbol to its strongest-pairing possibility. Equals calculateMinimumTm() when the primer has no degenerate symbol.
- calculateMinimumTm() : float
- The lowest melting temperature a degenerate primer could have, resolving every ambiguous symbol to its weakest-pairing possibility. Equals calculateMaximumTm() when the primer has no degenerate symbol.
- calculateNearestNeighborTm() : NearestNeighborTmResult
- Nearest-neighbor thermodynamics (SantaLucia 1998), Mg2+ converted into its sodium equivalent (von Ahsen et al. 2001), a self-complementary primer handled as such.
Methods
calculateGcPercent()
public
calculateGcPercent(string $sPrimer) : float
Parameters
- $sPrimer : string
Return values
float —Percentage, 0.0 for an empty primer
calculateMaximumTm()
The highest melting temperature a degenerate primer could have, resolving every ambiguous symbol to its strongest-pairing possibility. Equals calculateMinimumTm() when the primer has no degenerate symbol.
public
calculateMaximumTm(string $sPrimer) : float
Parameters
- $sPrimer : string
Return values
float —Degrees Celsius
calculateMinimumTm()
The lowest melting temperature a degenerate primer could have, resolving every ambiguous symbol to its weakest-pairing possibility. Equals calculateMaximumTm() when the primer has no degenerate symbol.
public
calculateMinimumTm(string $sPrimer) : float
Parameters
- $sPrimer : string
Return values
float —Degrees Celsius
calculateNearestNeighborTm()
Nearest-neighbor thermodynamics (SantaLucia 1998), Mg2+ converted into its sodium equivalent (von Ahsen et al. 2001), a self-complementary primer handled as such.
public
calculateNearestNeighborTm(string $sPrimer, float $iPrimerConcentration, float $iSaltConcentration, float $iMagnesiumConcentration) : NearestNeighborTmResult
Parameters
- $sPrimer : string
-
Must contain only A, C, G, T (either case) - no degenerate symbol
- $iPrimerConcentration : float
-
Total strand concentration, nM, positive
- $iSaltConcentration : float
-
Monovalent cations (Na+, K+), mM
- $iMagnesiumConcentration : float
-
Free Mg2+, mM