基因组注释文件(GTF/GFF)格式介绍

基因组注释文件GTF/GFF格式的介绍

GFF 2 -> GTF -> GFF 3                The GTF (General Transfer Format) is identical to GFF version 2 

GTF其实就是GFF版本2

其格式为（每个数字代表一列，总共9列）

1. seqname- （染色体名称）  name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix.

2. source- （用什么软件产生的）name of the program that generated this feature, or the data source (database or project name)

3. feature- （是转录本/外显子/内含子 等）feature type name, e.g. Gene, Variation, Similarity

4. start-（起始点） Start position of the feature, with sequence numbering starting at 1.

5. end- （终止点）End position of the feature, with sequence numbering starting at 1.

6. score- A floating point value.

7. strand (正链还是负链)- defined as + (forward) or - (reverse).

8. frame- One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..

9. attribute- （特性，比如编码的蛋白 等）A semicolon-separated list of tag-value pairs, providing additional information about each feature.

举例：

transcribed_pseudogene ------> gene ------> 11869 ------> 14409 ------> .------> +  ------>. ------> gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";

参考：

https://www.biostars.org/p/99462/

http://www.ensembl.org/info/website/upload/gff.html