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Old 08-14-2013, 12:28 AM   #1
kaiwang
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Cool 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?
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Old 08-14-2013, 01:54 AM   #2
rhinoceros
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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.
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Old 08-14-2013, 05:04 PM   #3
kaiwang
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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 View Post
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..
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Old 08-14-2013, 09:45 PM   #4
rhinoceros
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Quote:
Originally Posted by kaiwang View Post
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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