NCBI gene database question

Question

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?

Answer 1

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