Helix.energy: Calculates folding INN-HB parameters for a helix sequnece

In JPSieg/MeltR: Automated fitting of RNA/DNA absorbance melting curves and fluorescence binding isotherms in R

Calculates folding INN-HB parameters for a helix sequnece

Description

Calculates folding INN-HB parameters for a helix sequnece

Usage

Helix.energy(
  seqF = "ACGCA",
  seqR = "UGCGU",
  output = "df",
  F.Q = FALSE,
  Double.label = 0,
  Fluor = "FAM",
  Qunecher = "BHQ1",
  AA.UU = -0.9,
  AU.AU = -1.1,
  UA.UA = -1.3,
  CU.AG = -2.1,
  CA.UG = -2.1,
  GU.AC = -2.2,
  GA.UC = -2.1,
  CG.CG = -2.4,
  GG.CC = -3.3,
  GC.GC = -3.4,
  Initiation = 4.09,
  Term.AU = 0.45,
  FAMC.GBHQ1 = -3.93,
  FAMU.ABHQ1 = -3,
  FAMG.CBHQ1 = -4,
  FAMA.UBHQ1 = -2.5,
  Symmetry = 0.43
)

Arguments

seqF	Forward RNA sequence
seqR	Reverse RNA sequence
output	The format you want the data to be in. "df" for a dataframe counting the parameters or "energy" for the energy of folding.
F.Q	Is there a fluorophore or a quencher on the helix.
AA.UU	= -0.9, #UU.AA 1 Energy for a folding parameter
AU.AU	= -1.1,#AU.AU Energy for a folding parameter
UA.UA	= -1.3, #UA.UA Energy for a folding parameter
CU.AG	= -2.1, #AG.CU 2 Energy for a folding parameter
CA.UG	= -2.1, #UG.CA 3 Energy for a folding parameter
GU.AC	= -2.2, #AC.GU 4 Energy for a folding parameter
GA.UC	= -2.1, #UC.GA 5 Energy for a folding parameter
CG.CG	= -2.4, #CG.CG Energy for a folding parameter
GG.CC	= -3.3, #CC.GG 6 Energy for a folding parameter
GC.GC	= -3.4, #GC.GC Energy for a folding parameter
Initiation	= 4.09 Energy for a folding parameter
Term.AU	= 0.45 Energy for a folding parameter
FAMC.GBHQ1	= -3.93 Energy for a folding parameter
Symmetry	= 0.43 Energy for a folding parameter

Value

A data frame containing the data in the "information in the ".o3a" formatted file.

JPSieg/MeltR documentation built on Feb. 4, 2024, 7:10 a.m.