How to download all the bacterial protein data from NCBI?

kaiwang · 08-14-2013, 12:28 AM

Hi,

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

rhinoceros · 08-14-2013, 01:54 AM

ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.faa.tar.gz

Includes archaea. You could also make bacteria sub db from NR..

1. http://www.ncbi.nlm.nih.gov/protein/...;Organism:exp] > send to: file: gi list
2. blastdb_aliastool -gilist yourList.txt -db nr -out BacteriaOfNr -title BacteriaOfNr -dbtype prot

Another alternative would be to learn to use eutils..

kaiwang · 08-14-2013, 05:04 PM

Hi,rhinoceros

Thanks. I'll try to download the gi file first. Or maybe the seq file (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.faa.tar.gz) can provide me the id to filter the NR database.

I don't quite understand why use "txid2[Organism:exp]" to search for bacterial protein?

Kai

Quote:

Originally Posted by rhinoceros

ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.faa.tar.gz

Includes archaea. You could also make bacteria sub db from NR..

1. http://www.ncbi.nlm.nih.gov/protein/...;Organism:exp] > send to: file: gi list
2. blastdb_aliastool -gilist yourList.txt -db nr -out BacteriaOfNr -title BacteriaOfNr -dbtype prot

Another alternative would be to learn to use eutils..

rhinoceros · 08-14-2013, 09:45 PM

Quote:

Originally Posted by kaiwang

Hi,rhinoceros

I don't quite understand why use "txid2[Organism:exp]" to search for bacterial protein?

Because NCBI Taxonomy ID for Bacteria is "2"

http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

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08-14-2013, 12:28 AM	#1
kaiwang Junior Member Location: china Join Date: Aug 2013 Posts: 2	How to download all the bacterial protein data from NCBI? Hi, I want to do a local blast using all the bacterial protein data from NCBI instead of NR. Is there anyway to download all the data from NCBI? or to filter the NR database locally?

08-14-2013, 01:54 AM	#2
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.faa.tar.gz Includes archaea. You could also make bacteria sub db from NR.. 1. http://www.ncbi.nlm.nih.gov/protein/...;Organism:exp] > send to: file: gi list 2. blastdb_aliastool -gilist yourList.txt -db nr -out BacteriaOfNr -title BacteriaOfNr -dbtype prot Another alternative would be to learn to use eutils.. Last edited by rhinoceros; 08-14-2013 at 02:05 AM.