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.

Synopsis

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

Input
isdna:(Input)true for DNA, false for RNA
savesize:(Input)Size of array to save, or zero if none
Returns
void:No return value

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

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

Input
strand:(Input)Pointer to a sequence string
len:(Input)Length of sequence
shift:(Input)Stepping value
isDNA:(Input)DNA or RNA
maySave:(Input)May use the save arrays for speedup
Output
enthalpy:(Output)enthalpy
entropy:(Output)entropy
Returns
float:Melt energy

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltTemp

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

Synopsis

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

Input
strand:(Input)Pointer to a sequence string
len:(Input)Length of sequence
shift:(Input)Stepping value
saltconc:(Input)mM salt concentration
DNAconc:(Input)nM DNA concentration
isDNA:(Input)DNA or RNA
Returns
float:Melt temperature

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltGC

Calculates GC fraction of a sequence allowing for ambiguity

Synopsis

Prototype
float ajMeltGC (
      const AjPStr strand,
      ajint len
);

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

Input
strand:(Input)Pointer to a sequence string
len:(Input)Length of sequence
Returns
float:GC fraction

Description

Calculates GC fraction of a sequence allowing for ambiguity

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltEnergy2

Calculates melt energy for use with programs like prima

Giving this routine the complete sequence on the first call and setting meltInitDone to false will initialise the energy, entropy and enthalpy arrays. Subsequent calls will not look at the sequence directly.

Synopsis

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

Input
strand:(Input)Pointer to a sequence string
pos:(Input)Position within sequence
len:(Input)Length of sequence segment
isDNA:(Input)true if dna
Output
enthalpy:(Output)calculated enthalpy
entropy:(Output)calculated entropy
saveentr:(Output)entropy save array
saveenth:(Output)enthalpy save array
saveener:(Output)energy save array
Returns
float:melt energy

Description

Calculates melt energy for use with programs like prima

Giving this routine the complete sequence on the first call and setting meltInitDone to false will initialise the energy, entropy and enthalpy arrays. Subsequent calls will not look at the sequence directly.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltTempSave

Calculates melt temperature of DNA or RNA

Synopsis

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

Input
strand:(Input)Pointer to a sequence string
pos:(Input)position within sequence
len:(Input)Length of sequence (segment)
saltconc:(Input)mM salt concentration
DNAconc:(Input)nM DNA concentration
isDNA:(Input)DNA or RNA
Output
saveentr:(Output)entropy save array
saveenth:(Output)enthalpy save array
saveener:(Output)energy save array
Returns
float:Melt temperature

Description

Calculates melt temperature of DNA or RNA

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltTempProd

Calculates product melt temperature of DNA

Synopsis

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

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

Input
gc:(Input)GC percentage
saltconc:(Input)mM salt concentration
len:(Input)Length of sequence (segment)
Returns
float:Melt temperature

Description

Calculates product melt temperature of DNA

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAnneal

Calculates annealing temperature of product and primer

Synopsis

Prototype
float ajAnneal (
      float tmprimer,
      float tmproduct
);

TypeNameRead/WriteDescription
floattmprimerInputprimer Tm
floattmproductInputproduct Tm
float RETURNAnnealing temperature

Input
tmprimer:(Input)primer Tm
tmproduct:(Input)product Tm
Returns
float:Annealing temperature

Description

Calculates annealing temperature of product and primer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMeltExit

Cleans up DNA melting processing internal memory

Synopsis

Prototype
void ajMeltExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up DNA melting processing internal memory

See Also

See other functions in this section

Availability

In release 6.4.0