Do we need local databases?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Feb 14 06:41:32 EST 1995


the last posting in the 'GCG on a PC' thread raised an interesting 
hypothesis which I would like to get more input on. The author mentions that, 
due to the speed and ease of the NCBI network server, it were easy to 
omit local databases and rely on network resources entirely. 

We have seriously investigated this earlier and concluded that the 
work done by many of the 'casual' users (i.e., type in sequence, search 
sequence, retrieve top hit) can indeed be done by networked databases. 
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.

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?


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