How to download all the bacterial protein data from NCBI?

[kaiwang]

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]

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]

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

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]

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/Browser/wwwtax.cgi?mode=Info&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock