This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Download all NCBI gene names, synonyms, and gene ID for an organism

I would like to download all NCBI genes, synonyms and gene ID #s for mouse, and then human. Ive tried downloading lists of gene names, and then searching NCBI to get gene ID, however I run into problems with NCBI having a different official name compared to what I input. Is there a way to get all of the gene IDs easily in one go? Thanks!

gene
• 11,998 views • link
updated by Istvan Albert Istvan Albert • written by Patrick • Patrick

1 answer

Do you mean, you would like to download the complete reference from NCBI from the RefSeq FTP site?

like here for mouse and her for human

• 0 views • link
written by skbrimer skbrimer

I am only looking for a table or list. Something along the lines of:
Symbol Entrez Gene ID
Pzp 11287
Aanat 11298
Aatk 11302
Abca1 11303
Abca4 11304

(That has all Gene IDs)

• 0 views • link
written by Patrick • Patrick

Quite straightforward. For Mus musculus gene: go to the NCBI gene page >> https://www.ncbi.nlm.nih.gov/gene/?term=Mus+musculus and go to "send to" >> file >> tabular (text). Then open the file and select the column 3 and 6 and save to new table:

cat gene_result.txt  | cut -f3,6 > Mus_mus_gene_id.txt
• 0 views • link
written by lessismore lessismore

Wow, that was too easy. Exactly what I was looking for, Thank you!

• 0 views • link
written by Patrick • Patrick

Log in to answer this question.

More posts like this