Question: How to download all the parasite protein data from NCBI?
0
gravatar for najibveto
2.1 years ago by
najibveto30
Korea, Republic Of
najibveto30 wrote:

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?

protein parasite ncbi • 875 views
ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 2.1 years ago by najibveto30

thanks a lot for your help.

ADD REPLYlink written 2.1 years ago by najibveto30
2
gravatar for j_susat
2.1 years ago by
j_susat40
Kiel
j_susat40 wrote:

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
ADD COMMENTlink written 2.1 years ago by j_susat40
1
gravatar for natasha.sernova
2.1 years ago by
natasha.sernova3.3k
natasha.sernova3.3k wrote:

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..

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by natasha.sernova3.3k
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