nuget
NucleicAcid sequence property calculator
NucleicAcidStaticsProperty
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. |
| NucleotideFrequencies | 1 | |
| Count | 1 | |
| ATPercent | 1 |
03 Members
批量计算出GCSkew或者GC%
Parameters
| Name | Type | Description |
|---|---|---|
nts | IEnumerable(Of FastaSeq) | - |
winSize | Int32 | - |
steps | Int32 | - |
method | NtProperty | - |
GC_Content(
IEnumerable(Of DNA))Calculate the GC content of the target sequence data.
Parameters
| Name | Type | Description |
|---|---|---|
seq | IEnumerable(Of DNA) | - |
GetCompositionVector(
Char(), Double, Double, Double, Double)A, T, G, C
Parameters
| Name | Type | Description |
|---|---|---|
seq | Char() | - |
pA | Double | - |
pT | Double | - |
pG | Double | - |
pC | Double | - |
GetCompositionVector(
Char())A, T, G, C
Parameters
| Name | Type | Description |
|---|---|---|
Sequence | Char() | - |
Returns
A, T, G, C
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 |
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 |
Calculate the GC content of the target sequence data.
Parameters
| Name | Type | Description |
|---|---|---|
SequenceModel | IPolymerSequenceModel | - |
SlideWindowSize | Int32 | - |
Steps | Int32 | - |
Circular | Boolean | - |
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
Parameters
| Name | Type | Description |
|---|---|---|
SequenceModel | IPolymerSequenceModel | - |
SlideWindowSize | Int32 | - |
Steps | Int32 | - |
Circular | Boolean | - |
base | Char() | 必须是大写的字符 |
basePercent(
String, Int32, Char())Get content percentage value of the given nucleotide bases.
Parameters
| Name | Type | Description |
|---|---|---|
segment | String | - |
winSize | Int32 | - |
base | Char() | - |
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
NucleotideFrequencies(
String)Count(
String, Char())