ajdan.c
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 |
Input
isdna: | (Input) | true for DNA, false for RNA |
savesize: | (Input) | Size of array to save, or zero if none |
Returns
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
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 |
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
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
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
);
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
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
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 |
Input
strand: | (Input) | Pointer to a sequence string |
len: | (Input) | Length of sequence |
Returns
Description
Calculates GC fraction of a sequence allowing for ambiguity
See Also
See other functions in this section
Availability
In release 6.4.0
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 |
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
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
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
);
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
Description
Calculates melt temperature of DNA or RNA
See Also
See other functions in this section
Availability
In release 6.4.0
Calculates product melt temperature of DNA
Synopsis
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 |
Input
gc: | (Input) | GC percentage |
saltconc: | (Input) | mM salt concentration |
len: | (Input) | Length of sequence (segment) |
Returns
Description
Calculates product melt temperature of DNA
See Also
See other functions in this section
Availability
In release 6.4.0
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 |
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
Cleans up DNA melting processing internal memory
Synopsis
Prototype
void ajMeltExit (
void
);
Type | Name | Read/Write | Description |
void | | RETURN | |
Returns
Description
Cleans up DNA melting processing internal memory
See Also
See other functions in this section
Availability
In release 6.4.0