Question

Download all NCBI gene names, synonyms, and gene ID for an organism

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6.5 years ago

Patrick ▴ 10

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 • 10k views

ADD COMMENT • link updated 6.5 years ago by Istvan Albert 100k • written 6.5 years ago by Patrick ▴ 10

score 2 · Answer 1 · 2017-10-18

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6.5 years ago

skbrimer ▴ 740

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

ADD COMMENT • link 6.5 years ago by skbrimer ▴ 740

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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)

ADD REPLY • link 6.5 years ago by Patrick ▴ 10

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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