How to use efetch to download specific gene from whole genome NCBI by linux terminal?
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2.3 years ago
Ahmad ▴ 10

I need download specific gene from whole genome (like gene length from 11200 bp to 11350 bp) on linux terminal.

efetch NCBI terminal • 1.0k views
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You already have competent answers to your question, and this is not one of them. If I had to do the same for 500+ genes, I'd probably be looking for a similar solution as you have, because manual solutions would be so time-consuming. But for a single gene, I so would not trust the automated process because there are always things that can wrong. Unless this is for homework, how difficult is it to find a single gene on NCBI and manually excise the range of bases you need?

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I have large number of genes, manually is difficult

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2.3 years ago
vkkodali_ncbi ★ 3.7k

You can use EntrezDirect for this as follows:

$ esearch -db gene -query '11200:11350[gene length] AND "homo sapiens"[organism]'

This returns 192 genes that satisfy this criteria. You can then pipe the output of the above command to other EntrezDirect tools depending on your downstream analysis.

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