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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajMeltGC

Calculates GC fraction of a sequence allowing for ambiguity

Synopsis

Prototype

float ajMeltGC (
      const AjPStr strand,
      ajint len
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajProdTm

Calculates product melt temperature of DNA

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAnneal

Calculates annealing temperature of product and primer

Synopsis

Prototype

float ajAnneal (
      float tmprimer,
      float tmproduct
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajMeltExit

Cleans up DNA melting processing internal memory

Synopsis

Prototype

void ajMeltExit (
      void
);

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

See Also

See other functions in this section

Availability

In release 3.0.0