ajdan.c


Function ajMeltInit

Initialises melt entropies, enthalpies and energies. Different data files are read for DNA or RNA heteroduplex. Also sets optional flag for array saving of the above.

Prototype

void ajMeltInit (
      AjBool isdna,
      ajint savesize
);

TypeNameRead/WriteDescription
AjBoolisdnaInputtrue for DNA, false for RNA
ajintsavesizeInputSize of array to save, or zero if none
void RETURNNumber of energies to save

From EMBOSS 1.0.0


Function ajMeltEnergy

Calculates melt energy and enthalpy/entropy for a sequence string. An optional shift is given for stepping along the sequence and loading up energy arrays.

Prototype

float ajMeltEnergy (
      const AjPStr strand,
      ajint len,
      ajint shift,
      AjBool isDNA,
      AjBool maySave,
      float* enthalpy,
      float* entropy
);

TypeNameRead/WriteDescription
const AjPStrstrandInputPointer to a sequence string
ajintlenInputLength of sequence
ajintshiftInputStepping value
AjBoolisDNAInputDNA or RNA
AjBoolmaySaveInputMay use the save arrays for speedup
float*enthalpyOutputenthalpy
float*entropyOutputentropy
float RETURNMelt energy

From EMBOSS 1.0.0


Function ajMeltTemp

Calculates melt temperature of DNA or RNA An optional shift is given for stepping along the sequence and loading up energy arrays.

Prototype

float ajMeltTemp (
      const AjPStr strand,
      ajint len,
      ajint shift,
      float saltconc,
      float DNAconc,
      AjBool isDNA
);

TypeNameRead/WriteDescription
const AjPStrstrandInputPointer to a sequence string
ajintlenInputLength of sequence
ajintshiftInputStepping value
floatsaltconcInputmM salt concentration
floatDNAconcInputnM DNA concentration
AjBoolisDNAInputDNA or RNA
float RETURNMelt temperature

From EMBOSS 6.2.0


Function ajMeltGC

Calculates GC fraction of a sequence allowing for ambiguity

Prototype

float ajMeltGC (
      const AjPStr strand,
      ajint len
);

TypeNameRead/WriteDescription
const AjPStrstrandInputPointer to a sequence string
ajintlenInputLength of sequence
float RETURNGC fraction

From EMBOSS 1.0.0


Function ajMeltEnergy2

Calculates melt energy for use with programs like prima

Prototype

float ajMeltEnergy2 (
      const char* strand,
      ajint pos,
      ajint len,
      AjBool isDNA,
      float* enthalpy,
      float* entropy,
      float** saveentr,
      float** saveenth,
      float** saveener
);

TypeNameRead/WriteDescription
const char*strandInputPointer to a sequence string
ajintposInputPosition within sequence
ajintlenInputLength of sequence segment
AjBoolisDNAInputtrue if dna
float*enthalpyOutputcalculated enthalpy
float*entropyOutputcalculated entropy
float**saveentrOutputentropy save array
float**saveenthOutputenthalpy save array
float**saveenerOutputenergy save array
float RETURNmelt energy

From EMBOSS 1.0.0


Function ajMeltTempSave

Calculates melt temperature of DNA or RNA

Prototype

float ajMeltTempSave (
      const char* strand,
      ajint pos,
      ajint len,
      float saltconc,
      float DNAconc,
      AjBool isDNA,
      float** saveentr,
      float** saveenth,
      float** saveener
);

TypeNameRead/WriteDescription
const char*strandInputPointer to a sequence string
ajintposInputposition within sequence
ajintlenInputLength of sequence (segment)
floatsaltconcInputmM salt concentration
floatDNAconcInputnM DNA concentration
AjBoolisDNAInputDNA or RNA
float**saveentrOutputentropy save array
float**saveenthOutputenthalpy save array
float**saveenerOutputenergy save array
float RETURNMelt temperature

From EMBOSS 6.2.0


Function ajMeltTempProd

Calculates product melt temperature of DNA

Prototype

float ajMeltTempProd (
      float gc,
      float saltconc,
      ajint len
);

TypeNameRead/WriteDescription
floatgcInputGC percentage
floatsaltconcInputmM salt concentration
ajintlenInputLength of sequence (segment)
float RETURNMelt temperature

From EMBOSS 6.2.0


Function ajAnneal

Calculates annealing temperature of product and primer

Prototype

float ajAnneal (
      float tmprimer,
      float tmproduct
);

TypeNameRead/WriteDescription
floattmprimerInputprimer Tm
floattmproductInputproduct Tm
float RETURNAnnealing temperature

From EMBOSS 1.0.0


Function ajMeltExit

Cleans up DNA melting processing internal memory

Prototype

void ajMeltExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.0.0