Hello Bionetters,
It has become vitally important for molecular biologists to be able to rapidly
identify new sequences similar to theirs. Database searching programs such as
BLAST are very useful in this regard, but, with the vast amount of data being
produced, doing searches and browsing rather bulky result files to find novel
similarities is a very tedious task which must be repeated over and over again,
ideally as soon as new sequences have been incorporated into the database of
interest.
Honestly, haven't you ever dreamt that someone would keep the watch for you?
That's exactly what DBWatcher can do for you when run daily :
1) Search a database for similarities to your sequence(s)
when there has been an update since last search.
2) Browse results to find novel similarities.
3) Send these novel similarities by e-mail to you and/or
your colleagues and collaborators.
And if you do not have a direct access to BLAST programs and databases, don't
worry. You may ask a colleague or a collaborator to run DBWatcher for you and
you'll automatically receive the results in your e-mail box. And your colleague
doesn't even have to receive the results if he doesn't want to. This might suit
well a local area network with a server dedicated to sequence analysis or even a
BLAST searches e-mail or WWW server (why not? is anybody interested in setting
one up?).
At the moment, DBWatcher jobs can only be managed by hand or with SetDBWatcher,
which takes care of everything in a very user-friendly way thanks to its GUI.
SetDBWatcher is distributed along with DBWatcher and requires the Vibrant NCBI
ToolKit and Motif libraries.
>From the administrator's point of view, as DBWatcher can be run as a cron job
during slack periods it allows a more even redistribution of CPU usage.
Furthermore, as it does not perform unecessary searches by checking the time
stamps of database, sequences, configuration and last result files, DBWatcher
reduces CPU usage compared to a systematic search.
It is also possible to control the maximum number of simultaneous searches by
limiting the number of users authorized to run DBWatcher since results can be
sent to any e-mail address in the world, independantly of the user responsible
for running the program, and searches for one user are performed sequentially.
If you are interested in getting your own copy of DBWatcher you can download the
compressed archive at the following URL :
ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/dbwatcher.tar.Z
At the moment, I could only test DBWatcher on a Sparc 1000E running Solaris 2.5
with GCG versions of BLAST programs.
I would be glad to hear from any installation on or port to any other config.
Regards,
Frédéric PLEWNIAK
Bioinformatics
Strasbourg - FRANCE
