Models

Primer

Primer and it's key paramets.

Fields:

Name	Type	Description	Example	Default
seq	DNASeq	Sequence of the primer
location	Optional[Interval]	Location of the primer relative to target
target_id	Optional[str]	ID of the target sequence		null
tm	Optional[float]	Melting temperature of the primer		null
gc_content	Optional[float]	GC content of the primer sequence		null
self_binding_tm	Optional[float]	Melting temperature of any self-binding structures		null
hairpin_tm	Optional[float]	Melting temperature of primer hairpin		null
end_stability	Optional[float]	The maximal delta G for duplex dusruption of the last five three-prime bases in kcal/mol		null

PrimerPair

A pair of primers for running a PCR.

Fields:

Name	Type	Description	Example	Default
left	Primer
right	Primer
product_size	Optional[int]	Length of the PCR product		null
target_id	Optional[str]	ID of the target sequence		null

PCRConcentrations

Concentrations of the key components of the PCR reaction.

Fields:

Name	Type	Description	Example	Default
monovalent_salts	float	Conecentration (nM) of monovalent salts, e.g. KCl
divalent_salts	float	Conecentration (nM) of divalent salts, e.g. MgCl2+
dntps	float	Total concentration (nM) of dNTPs

Parameter3Range

Parameter range defined by a minimal, maximal and optimal values.

Fields:

Name	Type	Description	Example	Default
min	T	Minimal value
optimal	T	Optimal value
max	T	Maximal value

Parameter2Range

Parameter range defined by minimal and maximal values.

Fields:

Name	Type	Description	Example	Default
min	T	Minimal value
max	T	Maximal value

Interval

Sequence interval defined by a start position and lenght in bp.

Fields:

Name	Type	Description	Example	Default
start	int	Start of the interval	0
length	int	Length of the interval	10
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