[Biodevelopers] download bacterial genomes

[Titus Brown]

On Mon, Jun 19, 2006 at 05:45:22PM +0200, ibtissem grissa wrote:
-> >
-> >What about:
-> >
-> >ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria
-> 
-> yes, but I found only complete and published genomes there,
-> what I need is to have  the maximum of genomes, even if they are not
-> completed or public.
-> 
-> ?  Or you could look at TIGR and JGI sites; JGI in particular may have a
-> >few that aren't anywhere else.
-> 
-> 
-> And I need to download them by an automatic way, so how could I  check if
-> they don't exist elsewhere automatically.
-> 
-> Furthermore, I want to have all the information about genomes, and
-> especially the taxon classification of the organism
-> (Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
-> Enterobacteriaceae)

I don't actually know of an electronic source for that information,
although it may be possible to retrieve it from NCBI taxonomy.  I'm sure
if you browse around NCBI or TIGR you can find it.

Most microbial genomes get finished relatively quickly, because they're
so *tiny* ;).  I don't think there'll be much of a lag, so you might
want to just try out your algorithm on the already finished ones.

You can't get non-public ones ;).

In any case, if you do find a good source for all this information, please
repost it to this list (or send it to me personally ;).  I'd be very
interested.

thanks,
--titus