IUBio

Locally Mounted Databases

Ed Rybicki ed at MOLBIOL.UCT.AC.ZA
Tue Oct 29 00:59:31 EST 1996


> From:          ellis at vesicle.dental.upenn.edu (Ellis Golub)
> Subject:       Locally Mounted Databases

> Until recently, we mounted the full GCG database suite locally.  Then we ran
> out of disk space.  We are now considering whether to permanently stop
> mounting the databases locally, or to increase the disk capacity of our
> system to once again contain the databases.
> 
> I am intersted in the experiences/soutions taken by other sites.  In
> considering this issue, some users report that they can search the public
> databases more quickly than they had been able to search the local databases
> previously, and they worry that as the size increases, searching speed will
> decrease further. 

Greetings from the DEEEEEEP South....

We used to buy in the full GCG database, in the days when we had 
money, and international Internet access was painfully slow.  Now we 
have no money, bandwidth and speed of access have radically improved, 
and we no longer bother (and have not for two years) to get a 
database.  We find the database that still seems to come with the 
software updates provides an excellent basis from which to work - and 
if users come up with hits from BLAST or Entrez searches that are not 
in the database, then we point them in the general direction of the 
NCBI Web site.  Even though we are on the wrong end of a 10 000 km+ 
landline from the US, we still find BLAST and Entrez searches are 
relatively quick and easy - even when the US has woken up, in our 
afternoon. 

In fact, we are seriously thinking of not bothering to mount the
database at all, given ease of international access to the sequences
in question: I have been able to build locally BLAST-searchable
databases from current Genbank entries using a local FASTA-format
save file from the Taxonomy subsection of the Genbank database, via
the NCBI Web site, that comprises all potyvirus, carlavirus,
capillovirus and trichovirus sequences.  This may not be the 
preferred solution for people working with human or E coli sequences, 
but then, they would probably be doing BLAST searches on the current 
database via the Internet anyway.

Hope this helps,


                     Ed Rybicki, PhD  
      Dept Microbiology     |   ed at molbiol.uct.ac.za   
   University of Cape Town  | rybicki at uctvms.uct.ac.za
   Private Bag, Rondebosch  |  phone: x27-21-650-3265
      7700, South Africa    |   fax: x27-21-689 7573
    WWW URL: http://www.uct.ac.za/microbiology/ed.html      
                                        
    "Out here on the perimeter, there are no stars..."



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