[Bioclusters] download blast db with rsync in uncompressed format

[Josh Goodman]

The NCBI has a program called fmerge which lets you merge update files
into the blast databases instead of downloading the entire set each night.
However, it doesn't handle duplication so you will need to re-download the
complete set once a month or so to flush dups out.  Take a look at
ftp://ftp.ncbi.nih.gov/blast/db/README for more information.

Josh Goodman
Center for Genomics and Bioinformatics
Indiana University

On Mon, 1 Dec 2003 bioclusters-request@bioinformatics.org wrote:

> From: Fabien Steinmetz <fabienst@yahoo.fr>
> To: bioclusters@bioinformatics.org
> Date: Mon, 1 Dec 2003 10:30:39 +0100
> Subject: [Bioclusters] download blast db with rsync in uncompressed format
> Reply-To: bioclusters@bioinformatics.org
>
> Hello,
>
> We have to download the ncbi blast databases for use with blast on our
> cluster.
> We don't like the idea of having to download the whole database each time and
> would like to download only the changes. We found rsync which is a pretty
> good solution for that. So the problem was to find a server containing the
> data we wish to download. And there is bio-mirror.net. However on this server
> I can only find the preformatted databases in a compressed format (.gz).
>
> The problem is this one :
> in fact rsync can't be used at its "best performances" because the databases
> are already compressed. Thus the transmitted data to update a local version
> is very high and could be much lower if using rsync with uncompressed
> databases (by usind the rsync switch to compress data that is being
> transmitted).
> Is there any server on which it would be possible to get such uncompressed
> files (in fasta or precompressed format) ? I couldn't find any with a google.
> Or do you know a better way to lower the transmitted data ?
>
> Thanks
>
> Fabien
>
>
>
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