NCBI基因数据库问题(NCBI gene database question)

NCBI基因数据库问题(NCBI gene database question)

我试图找到基因名称和染色体位置的gene_info文件。 但是，我似乎无法在NCBI FTP站点上找到它。 任何人都可以给我一个指针？

I m trying to find gene_info file with genenames and chromosomal location. However, I can't seem to locate it on NCBI FTP site. Can anyone give me a pointer?

最满意答案

请参阅： ftp : //ftp.ncbi.nlm.nih.gov/gene/DATA/README了解有关NCBI ftp站点上的哪些文件的详细信息。

如果你想从NCBI本身获取数据，你需要合并多个文件，可能是一个gene2accession（它也包含位置信息）和一个gene_info文件，它将id映射为符号和名称等。

为了获得这些信息，到UCSC网站可能会更方便，如果您想了解可用的内容，他们还提供了一个公共mysql数据库： http : //workshops.arl.arizona.edu/sql1/sql_workshop/mysql/mysqlclient html的

如果您只需要人类，小鼠或大鼠的数据，那么大鼠基因组数据库已经编译了您想要的数据（来自NCBI和Ensembl资源的全新数据）： ftp : //rgd.mcw.edu/pub/data_release

例如，对于人类数据，请看： ftp : //rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt

See: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README for details of what is in what files at the NCBI ftp site.

If you want to get the data from NCBI itself you will need to combine multiple files, probably a gene2accession (which also includes position information) and a gene_info file which maps ids to symbols and names etc.

It is probably more convenient to go to the UCSC site for this information, they also provide a public mysql database if you want to explore what is available: http://workshops.arl.arizona.edu/sql1/sql_workshop/mysql/mysqlclient.html

If you just want human, mouse or rat data then the Rat Genome Database has already compiled the data you want (fresh from the NCBI and Ensembl sources): ftp://rgd.mcw.edu/pub/data_release

e.g. for human data look at: ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt