local database need

Steve Thompson: VADMS genetics THOMPSON at JAGUAR.CSC.WSU.EDU
Tue Feb 14 12:27:33 EST 1995

Hello folk -

In <1995Feb14.114132.19915 at comp.bioz.unibas.ch> Reinhard Doelz 
<doelz at comp.bioz.unibas.ch> argues for the importance of locally maintained

>.... However, to the residual 30% of users, who do not stop after having 
>noticed merely insignificant hits, what  happens if (1) you need to search for
>subsets in the database, (2) you need _many_ database entries  (i.e., a 100 or
>1000)  and (3) you do many comparisons, statistical or  evolutionary analysis,
>and individual work which should be done anyhow after a reasonable search.

Even though we may be in the minority, I wholeheartedly agree with Reinhard. 
Local databases enable these more complex analyses to be a trivial affair. 
Additionally, local databases enable the VERY novice user to run just a couple
of GCG programs, e.g. Fetch and BestFit, and get answers.  They do not have to
concern themselves with the intricacies of sequence format conversions nor
internet access.  Granted various mail server scripts exist to handle this but 
it is convenient for everybody to have the data home.  Furthermore, local
databases REDUCE network traffic and provide backup/alternative sites.  Let's
all do our part to conserve bandwidth.  :^)  Reinhard continues:

>One of my favourites is to use GCG's feature of files of sequence names 
>in order to group sequences and process these in any other operation. 
>Unless you have a very sophisticated network system, this can only be 
>achieved if your database is in the same environment as your process runs
>on local resources most of the time. In order to have _this_ achieved 
>with networks, we needed a much more sophisticated way to communicate 
>the search set which we want to tackle. I don't think of database 
>divisions here but of sets of data which do not use the whole length 
>but rather a short fragment of it . 
>How would you imagine to run this type of search in a networked environment?

Right on, GCG's list file format is the proverbial `best thing since sliced
bread.'  I try to get all my clients to take advantage of this feature.  Why
store sequences in your own account when they're right there in a local
database available at any moment?  Naturally, one needs to store their own
algined data, but it doesn't make sense to fill up your own account's quota
with raw sequence data.

					Just my $0.02 worth - Steve

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                   INTERnet:  THOMPSON at jaguar.csc.wsu.edu

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net