Extensions

Full name SMRUCC.genomics.ContextModel.Promoter.Extensions Assembly SMRUCC.genomics.Core Members 3

01 Syntax

SMRUCC.genomics.ContextModel.Promoter.Extensions

02 Methods

Name	Overloads	Summary
GetPrefixLengths	1	Read from PrefixLength members.
ParseUpstreamByLength	1	解析出所有基因前面的序列片段
GetUpstreamSeq	1	Get upstream nt sequence in a specific length for target gene.

03 Members

method GetPrefixLengths #

GetPrefixLengths

Read from PrefixLength members.

method ParseUpstreamByLength #

ParseUpstreamByLength(PTT, IPolymerSequenceModel, Int32, Int32)

解析出所有基因前面的序列片段

Parameters

Name	Type	Description
`context`	PTT	-
`nt`	IPolymerSequenceModel	-
`length%`	`Int32`	-
`minLen%`	`Int32`	最小有效间区长度（bp）。当上游调控区候选区间与上游基因的终止密码子重叠、且二者之间的间区小于该阈值时，对应基因返回空序列并标记 "intergenic too short"。详见 Extensions.GetUpstreamSeq()。

method GetUpstreamSeq #

GetUpstreamSeq``1(``0, GenomeContext(Of ``0), IPolymerSequenceModel, Int32, Int32)

Get upstream nt sequence in a specific length for target gene.

Remarks

(在这个函数之中，位点的计算的时候会有一个碱基的偏移量是因为为了不将起始密码子ATG之中的A包含在结果序列之中)

The extraction strategy is overlap-aware:

Compute the candidate region of len bp upstream of gene B's TSS.
If this region does not overlap the upstream gene A's stop codon, the full len bp is taken directly.
Otherwise the regulatory region is reduced to the intergenic spacer between gene A's stop codon and gene B's TSS. When that spacer is shorter than minLen an empty sequence tagged "intergenic too short" is returned (the two genes may be co-regulated).

Parameters

Name	Type	Description
`gene`	``0	The target gene (gene B) whose upstream regulatory region will be extracted.
`context`	GenomeContext(Of ``0)	The genome gene context, used to locate the transcriptionally upstream neighbour gene (gene A) via GenomeContext.GetDirectionalNeighbours().
`nt`	IPolymerSequenceModel	The genomic nucleotide sequence (circular aware).
`len%`	`Int32`	The desired length of the upstream regulatory region, measured from the transcription start site (TSS, i.e. the ATG end of gene).
`minLen%`	`Int32`	The minimal effective length of the intergenic spacer. When the candidate region overlaps the upstream gene A's stop codon, the regulatory region is reduced to the intergenic spacer (gene A stop codon -> gene B TSS). If that spacer is shorter than minLen the extraction is skipped and an empty FastaSeq tagged "intergenic too short" is returned.