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
);

Type Name Read/Write Description

AjBool isdna Input true for DNA, false for RNA

ajint savesize Input Size of array to save, or zero if none

void RETURN Number of energies to save

Type	Name	Read/Write	Description
`AjBool`	`isdna`	Input	true for DNA, false for RNA
`ajint`	`savesize`	Input	Size of array to save, or zero if none
`void`		RETURN	Number 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
);

Type Name Read/Write Description

const AjPStr strand Input Pointer to a sequence string

ajint len Input Length of sequence

ajint shift Input Stepping value

AjBool isDNA Input DNA or RNA

AjBool maySave Input May use the save arrays for speedup

float* enthalpy Output enthalpy

float* entropy Output entropy

float RETURN Melt energy

Type	Name	Read/Write	Description
`const AjPStr`	`strand`	Input	Pointer to a sequence string
`ajint`	`len`	Input	Length of sequence
`ajint`	`shift`	Input	Stepping value
`AjBool`	`isDNA`	Input	DNA or RNA
`AjBool`	`maySave`	Input	May use the save arrays for speedup
`float*`	`enthalpy`	Output	enthalpy
`float*`	`entropy`	Output	entropy
`float`		RETURN	Melt 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
);

Type Name Read/Write Description

const AjPStr strand Input Pointer to a sequence string

ajint len Input Length of sequence

ajint shift Input Stepping value

float saltconc Input mM salt concentration

float DNAconc Input nM DNA concentration

AjBool isDNA Input DNA or RNA

float RETURN Melt temperature

Type	Name	Read/Write	Description
`const AjPStr`	`strand`	Input	Pointer to a sequence string
`ajint`	`len`	Input	Length of sequence
`ajint`	`shift`	Input	Stepping value
`float`	`saltconc`	Input	mM salt concentration
`float`	`DNAconc`	Input	nM DNA concentration
`AjBool`	`isDNA`	Input	DNA or RNA
`float`		RETURN	Melt 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
);

Type Name Read/Write Description

const AjPStr strand Input Pointer to a sequence string

ajint len Input Length of sequence

float RETURN GC fraction

Type	Name	Read/Write	Description
`const AjPStr`	`strand`	Input	Pointer to a sequence string
`ajint`	`len`	Input	Length of sequence
`float`		RETURN	GC 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
);

Type Name Read/Write Description

const char* strand Input Pointer to a sequence string

ajint pos Input Position within sequence

ajint len Input Length of sequence segment

AjBool isDNA Input true if dna

float* enthalpy Output calculated enthalpy

float* entropy Output calculated entropy

float** saveentr Output entropy save array

float** saveenth Output enthalpy save array

float** saveener Output energy save array

float RETURN melt energy

Type	Name	Read/Write	Description
`const char*`	`strand`	Input	Pointer to a sequence string
`ajint`	`pos`	Input	Position within sequence
`ajint`	`len`	Input	Length of sequence segment
`AjBool`	`isDNA`	Input	true if dna
`float*`	`enthalpy`	Output	calculated enthalpy
`float*`	`entropy`	Output	calculated entropy
`float**`	`saveentr`	Output	entropy save array
`float**`	`saveenth`	Output	enthalpy save array
`float**`	`saveener`	Output	energy save array
`float`		RETURN	melt 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
);

Type Name Read/Write Description

const char* strand Input Pointer to a sequence string

ajint pos Input position within sequence

ajint len Input Length of sequence (segment)

float saltconc Input mM salt concentration

float DNAconc Input nM DNA concentration

AjBool isDNA Input DNA or RNA

float** saveentr Output entropy save array

float** saveenth Output enthalpy save array

float** saveener Output energy save array

float RETURN Melt temperature

Type	Name	Read/Write	Description
`const char*`	`strand`	Input	Pointer to a sequence string
`ajint`	`pos`	Input	position within sequence
`ajint`	`len`	Input	Length of sequence (segment)
`float`	`saltconc`	Input	mM salt concentration
`float`	`DNAconc`	Input	nM DNA concentration
`AjBool`	`isDNA`	Input	DNA or RNA
`float**`	`saveentr`	Output	entropy save array
`float**`	`saveenth`	Output	enthalpy save array
`float**`	`saveener`	Output	energy save array
`float`		RETURN	Melt temperature

From EMBOSS 6.2.0

Function ajMeltTempProd

Calculates product melt temperature of DNA

Prototype

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

Type Name Read/Write Description

float gc Input GC percentage

float saltconc Input mM salt concentration

ajint len Input Length of sequence (segment)

float RETURN Melt temperature

Type	Name	Read/Write	Description
`float`	`gc`	Input	GC percentage
`float`	`saltconc`	Input	mM salt concentration
`ajint`	`len`	Input	Length of sequence (segment)
`float`		RETURN	Melt temperature

From EMBOSS 6.2.0

Function ajAnneal

Calculates annealing temperature of product and primer

Prototype

float ajAnneal (
      float tmprimer,
      float tmproduct
);

Type Name Read/Write Description

float tmprimer Input primer Tm

float tmproduct Input product Tm

float RETURN Annealing temperature

Type	Name	Read/Write	Description
`float`	`tmprimer`	Input	primer Tm
`float`	`tmproduct`	Input	product Tm
`float`		RETURN	Annealing temperature

From EMBOSS 1.0.0

Function ajMeltExit

Cleans up DNA melting processing internal memory

Prototype

void ajMeltExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0