NucleicAcidStaticsProperty

Full name SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcidStaticsProperty Assembly SMRUCC.genomics.Core Members 11

NucleicAcid sequence property calculator

01 Syntax

SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcidStaticsProperty

02 Methods

Name	Overloads	Summary
GCData	1	批量计算出GCSkew或者GC%
GC_Content	1	Calculate the GC content of the target sequence data.
GetCompositionVector	2	A, T, G, C
GCContent	3	Calculate the GC content of the target sequence data.
Tm	1	The melting temperature of P1 is Tm(P1), which is a reference temperature for a primer to perform annealing and known as the Wallace formula
ContentCommon	1
basePercent	1	Get content percentage value of the given nucleotide bases.
GCSkew	1	Calculation the GC skew of a specific nucleotide acid sequence.

03 Members

method GCData #

GCData(IEnumerable(Of FastaSeq), Int32, Int32, NtProperty)

批量计算出GCSkew或者GC%

Parameters

Name	Type	Description
`nts`	`IEnumerable(Of FastaSeq)`	-
`winSize`	`Int32`	-
`steps`	`Int32`	-
`method`	NtProperty	-

method GC_Content #

GC_Content(IEnumerable(Of DNA))

Calculate the GC content of the target sequence data.

Parameters

Name	Type	Description
`seq`	`IEnumerable(Of DNA)`	-

method GetCompositionVector #

GetCompositionVector(Char(), Double, Double, Double, Double)

A, T, G, C

Parameters

Name	Type	Description
`seq`	`Char()`	-
`pA`	`Double`	-
`pT`	`Double`	-
`pG`	`Double`	-
`pC`	`Double`	-

method GetCompositionVector overload 2 #

GetCompositionVector(Char())

A, T, G, C

Parameters

Name	Type	Description
`Sequence`	`Char()`	-

Returns

A, T, G, C

method GCContent overload 2 #

GCContent(IPolymerSequenceModel)

Calculate the GC content of the target sequence data.

Parameters

Name	Type	Description
`Sequence`	IPolymerSequenceModel	序列数据大小写不敏感

method GCContent overload 3 #

GCContent(String)

Calculate the GC content of the target sequence data.

Parameters

Name	Type	Description
`NT`	`String`	序列数据大小写不敏感

method GCContent #

GCContent(IPolymerSequenceModel, Int32, Int32, Boolean)

Calculate the GC content of the target sequence data.

Parameters

Name	Type	Description
`SequenceModel`	IPolymerSequenceModel	-
`SlideWindowSize`	`Int32`	-
`Steps`	`Int32`	-
`Circular`	`Boolean`	-

method Tm #

Tm(String)

The melting temperature of P1 is Tm(P1), which is a reference temperature for a primer to perform annealing and known as the Wallace formula

method ContentCommon #

ContentCommon(IPolymerSequenceModel, Int32, Int32, Boolean, Char())

Parameters

Name	Type	Description
`SequenceModel`	IPolymerSequenceModel	-
`SlideWindowSize`	`Int32`	-
`Steps`	`Int32`	-
`Circular`	`Boolean`	-
`base`	`Char()`	必须是大写的字符

method basePercent #

basePercent(String, Int32, Char())

Get content percentage value of the given nucleotide bases.

Parameters

Name	Type	Description
`segment`	`String`	-
`winSize`	`Int32`	-
`base`	`Char()`	-

method GCSkew #

GCSkew(IPolymerSequenceModel, Int32, Int32, Boolean)

Calculation the GC skew of a specific nucleotide acid sequence. (对核酸链分子计算GC偏移量，请注意，当某一个滑窗区段内的GC是相等的话，则会出现正无穷)

Parameters

Name	Type	Description
`sequence`	IPolymerSequenceModel	Target sequence object should be a nucleotide acid sequence.(目标对象必须为核酸链分子)
`isCircular`	`Int32`	-

Returns

返回的矩阵是每一个核苷酸碱基上面的GC偏移量