Automatic Biological Database searches...

Keith James k.james at bangor.ac.uk
Fri Aug 1 04:47:27 EST 1997


Simon Twigger <simont at post.its.mcw.edu> writes:

> 
> Hi there, 
> 
> 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.
> 
> If such a thing doesnt exist, what do people think about the concept? I
> have a few applications for such a script and Im thinking of trying to
> write one, but if one already exists then theres not much point
> reinventing the wheel (unless the wheel costs a fortune ;).
> 
> If anyone has any comments or suggestions on the idea, Id love to hear
> them, preferably by email as I dont check the newsgroups too often.

There is such a beast, called FastAlert, that "performs periodic scans of
permanently updated protein or DNA databanks with user-supplied query
sequences". After a quick search I haven't been able to find a URL or ftp
site to download the source from, but it does exist.

Writing a script is the best alternative and has the benefit of doing
exactly what you want it to. It's something that I'm looking into as I
need a new project to hone my Perl.

-- 
Keith James Ph.D. - k.james at bangor.ac.uk  PGP 2.6.2i  Key ID 469A9FA1
Biodegradation Group                         *Encrypt and Survive*  
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