Automatic Biological Database searches...

Frederic PLEWNIAK plewniak at igbmc.u-strasbg.fr
Fri Aug 1 06:36:42 EST 1997


Hi,

> I was wondering if there is any software/scripts out there that will run
> a database search of the usual databases (GenBank, SwissProt etc.)
> automatically. The idea being that you dont have to rerun your favourite
> search criteria every week, the script does it for you and tells you if
> anything new has arrived.
> 
What kind of search? A search for keywords or for sequence similarity?

Sequence annotations and comments can be automatically searched with
the MIPS Alert Web Service (which uses the ATLAS retrieval system) at :

	http://www.mips.biochem.mpg.de/mips/programs/alert.html

...any others ? ...


For sequence similarity searches, may I suggest my own little thingy,
DBWatcher, which is able to run Blast searches automatically when the
database of interest has been updated (it checks this first). It can
run local searches on locally maintained databases or remote searches
on the NCBI Blast2 server and sends new similarities by e-mail.
It has been successfully compiled on Solaris, Digital Unix, Irix and
Linux. A port to VMS has been done recently by Susan Gottesman from NYU
but I haven't had much time to get deeper into it myself. 

You may read more about DBWatcher at :

	http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/

and download the source or binaries for your system at

	ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher


Regards,
Fred

Frédéric PLEWNIAK
Bioinformatics
I.G.B.M.C.
Strasbourg - France




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