SequenceAnalysis.StackingEnergy: SequenceAnalysis.StackingEnergy
In SequenceAnalysis: Sequence Analysis

Description Usage Arguments Details Value Author(s) Examples

Stacking Energy obtained by NN model

1 2	SequenceAnalysis.StackingEnergy(Nucleotide_Sequence = NULL, UniprotKB = NULL, CDS = TRUE)

`Nucleotide_Sequence`	Nucleotide Sequence
`UniprotKB`	UniProt ID of desired sequence
`CDS`	if TRUE Stacking Energy of CDS Region will be calculated

The NN model for nucleic acids assumes that the stability of a given base pair depends on the identity and orientation of neighboring base pairs. Stacking Energy = DeltaG(total) = Sigma (n(i)*DeltaG(i)) + DeltaG(init) + DeltaG(end) + DeltaG(sym), which DeltaG for i, init and end is obtained by Unified NN free energy parameter. Symmetry of self-complementary duplexes is also included by DeltaG(sym) equals to +0.43 kcal/mol if the duplex is self-complementary and zero if it is non-self-complementary.

StackingEnergy

Babak Khorsand

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SequenceAnalysis.StackingEnergy("actagtcacgatcag")
SequenceAnalysis.StackingEnergy(UniprotKB="O15131")
SequenceAnalysis.StackingEnergy(UniprotKB="O15131",CDS=FALSE)