How to download all the parasite protein data from NCBI?
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4.9 years ago
najibveto ▴ 60

I want to do a local blast using all the bacterial protein data from NCBI instead of NR. Is there any way to download all the data from NCBI? Or to filter the NR database locally?

parasite protein ncbi • 2.0k views
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thanks a lot for your help.

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4.9 years ago
j_susat ▴ 40

Hello,

if you just want to Download all the bacterial proteins from NCBI you could use Entrez Direct: Click Here Here is some small example which could do the job (restricted to refseq)

esearch -db protein -query "bacteria [ORGN] AND refseq [filter]" | efetch -format fasta > bacterial_proteins
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4.9 years ago
natasha.sernova ★ 3.9k

See this post and my answer inside:

where can I get environmental bacteria genome in fasta format (as many as possible)?

NCBI structure has been changed, so I am not sure about recent archives.

But to find at least something see ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/

and all.faa.tar.gz file. I don't know where to find a current version. The old one is from 02.06.2015..

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