On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith
<mike.dyallsm...@gmail.com> wrote:
> Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the
> files within their decompressed folders or do I put all the individual files
> into one folder? I assume the former, but want to be sure.
> Thanks again, Mike DS

Hi Mike,

Unless you're using a Graphical decompression tool which is trying
to be too helpful, each tar-ball does *not* decompress into its own
folder. The files should all be in the *same* folder.

I use this to verify the checksums,

$ md5sum --check nr.00.tar.gz.md5
nr.00.tar.gz: OK

Then I use this to decompress the tar-balls,

$ tar -zxvf nr.00.tar.gz

(Actually I don't do this personally any more - it has been setup
to happen automatically when the NCBI update the databases.)

We keep all our NCBI databases in the same folder,

$ ls /data/blastdb/ncbi/nr.*

We can then refer to the NR database at the command line
as /data/blastdb/ncbi/nr or as just nr if the BLAST database
path is configured to check this folder.

In this folder we also have other NCBI database, like NT:

$ ls /data/blastdb/ncbi/nt.*

Note you don't need to keep the *.tar.gz and the *.md5 files
once you've verified the checksum (using md5sum to detect
any data corruption during download) and decompressed the


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