Question

Download NCBI compiled protein database for specific genus

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13 months ago

saadleeshehreen ▴ 140

Hi,

How to download NCBI compiled protein database for specific genus ( eg. Acinetobacter baumannii) in a local computer?

protein NCBI • 526 views

ADD COMMENT • link updated 13 months ago by GenoMax 141k • written 13 months ago by saadleeshehreen ▴ 140

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You can also use ncbi datasets on the the command line or use one of other programs like Kai Blin's NCBI Genome downloader: https://github.com/kblin/ncbi-genome-download

ADD REPLY • link 13 months ago by GenoMax 141k

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Thanks. I just wanted to download all protein sequences for this specific species. Is there any way for command line?

ADD REPLY • link 13 months ago by saadleeshehreen ▴ 140

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Command line options are mentioned above. Here is a direct link to NCBI Datasets command line tool: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/

ADD REPLY • link 13 months ago by GenoMax 141k

score 3 · Answer 1 · 2023-03-27

Few different ways. Easiest is to use NCBI Datasets. There are multiple genomes available so go here: https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=470

Choose the genome you want. If you don't know specifically use the one with green check mark.

Pick genome

And then download using the appropriate check boxes (genbank or refseq etc).

Download