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genPred格式是table分割的,在Genome Browser中用于记录基因预测信息的常用形式。常见的genePred及变种对应如下:
Gene Predictions
table genePred
"A gene prediction."
(
string name: "Name of gene" //基因名称
string chrom: "Chromosome name" //染色体名称
char[1] strand: "+ or - for strand" //正负链信息
uint txStart: "Transcription start position" //转录起始位点
uint txEnd: "Transcription end position" //转录终止位点
uint cdsStart: "Coding region start" //编码区起始位点
uint cdsEnd: "Coding region end" //编码区终止位点
uint exonCount: "Number of exons" //外显子数量
uint[exonCount] exonStarts: "Exon start positions" //外显子起始位点
uint[exonCount] exonEnds: "Exon end positions" //外显子终止位点
)
Gene Predictions(Extended)
table genePred
"A gene prediction."
(
string name: "Name of gene (usually transcript_id from GTF)" //基因名称,通常是GTF中的转录本ID
string chrom: "Chromosome name" //染色体名称
char[1] strand: "+ or - for strand" //正负链信息
uint txStart: "Transcription start position" //转录起始位点
uint txEnd: "Transcription end position" //转录终止位点
uint cdsStart: "Coding region start" //编码区起始位点
uint cdsEnd: "Coding region end" //编码区终止位点
uint exonCount: "Number of exons" //外显子数量
uint[exonCount] exonStarts: "Exon start positions" //外显子起始位点
uint[exonCount] exonEnds: "Exon end positions" //外显子终止位点
int score: "Score" //得分
string name2: "Alternate name"(e.g. gene_id from GTF) //别名,一般是GTF中的Gene ID
string cdsStartStat: "Status of CDS start annotation (none, unknown, incomlete, or complete)" //CDS起始位点注释信息,包括没有,未知,完整和不完整
string cdsEndStat: "Status of CDS end annotation (none, unknown, incomlete, or complete)" //CDS终止位点注释信息,包括没有,未知,完整和不完整
IstringexonFrames: "Exon frame offsets [0,1,2]" //外显子框架位置
)
Gene Predictions and RefSeq Genes with Gene Names
在该模式下,如果存在可变剪切,则每个转录本一行
table genePred
"A gene prediction."
(
string geneName: "Name of gene as it appears in Genome Browser." //Genome Browser 中的基因名称
string name: "Name of gene" //基因名称
string chrom: "Chromosome name" //染色体名称
char[1] strand: "+ or - for strand" //正负链信息
uint txStart: "Transcription start position" //转录起始位点
uint txEnd: "Transcription end position" //转录终止位点
uint cdsStart: "Coding region start" //编码区起始位点
uint cdsEnd: "Coding region end" //编码区终止位点
uint exonCount: "Number of exons" //外显子数量
uint[exonCount] exonStarts: "Exon start positions" //外显子起始位点
uint[exonCount] exonEnds: "Exon end positions" //外显子终止位点
)
转自:
https://www.bilibili.com/read/cv7613234/