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
);

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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajProbScore

Gives a score for the probability of two sequences being the same. The sequences are the same length. Uses IUB ambiguity codes. The result is the sum of the probabilities at each position.

Synopsis

Prototype

float ajProbScore (
      const AjPStr seq1,
      const AjPStr seq2,
      ajint len
);

Type Name Read/Write Description

const AjPStr seq1 Input Pointer to a sequence string

const AjPStr seq2 Input Pointer to a another sequence

ajint len Input Length of sequences

float RETURN Match probability

Type	Name	Read/Write	Description
const AjPStr	seq1	Input	Pointer to a sequence string
const AjPStr	seq2	Input	Pointer to a another sequence
ajint	len	Input	Length of sequences
float		RETURN	Match probability

Input

seq1:	(Input)	Pointer to a sequence string
seq2:	(Input)	Pointer to a another sequence
len:	(Input)	Length of sequences

Returns

float:

Match probability

Description

Gives a score for the probability of two sequences being the same. The sequences are the same length. Uses IUB ambiguity codes. The result is the sum of the probabilities at each position.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajTm

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 ajTm (
      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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMeltGC

Calculates GC fraction of a sequence allowing for ambiguity

Synopsis

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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
);

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajTm2

Calculates melt temperature of DNA or RNA

Synopsis

Prototype

float ajTm2 (
      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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajProdTm

Calculates product melt temperature of DNA

Synopsis

Prototype

float ajProdTm (
      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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajAnneal

Calculates annealing temperature of product and primer

Synopsis

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

Input

tmprimer:	(Input)	primer Tm
tmproduct:	(Input)	product Tm

Returns

float:

Annealing temperature

Description

Calculates annealing temperature of product and primer

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMeltExit

Cleans up DNA melting processing internal memory

Synopsis

Prototype

void ajMeltExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Cleans up DNA melting processing internal memory

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

ajdan.c

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