EMBNet News bulletin of 23-Sep-1997

Victor Jongeneel Victor.Jongeneel at isrec.unil.ch
Tue Sep 23 14:16:41 CEST 1997

* EMBNet News bulletin of 23-Sep-1997 *

1. New profile scan service

We have completely updated our Profile scan service on the Web 
(http://www.ch.embnet.org/software/PFSCAN_form.html ). This service will 
scan your protein sequence for the occurrence of generalized profiles from 
the ISREC collection (profiles destined to be added to, or already present 
in the Prosite database), or derived from Erik Sonnhammer and Sean Eddy's 
PfamA collection of hidden Markov models (more than 500 HMMs). These two 
profile databases are partially redundant, but were independently derived. 
The PfamA collection is more complete for motifs occurring in extracellular 
domains, while the ISREC collection contains many new motifs from proteins 
involved in signal transduction.

The pfscan program runs on the INSECTs, our supercomputer based on 16 
networked low-cost PCs. It is to our knowledge the fastest available server 
to scan protein sequences for the occurrence of complex motifs. See the 
latest issue of the embnet.news newsletter (Sept. 1997, to be released 
soon) for details.

2. New GCG machine.

The SGI Origin2000 server made available to us by the Sections of Pharmacy 
and Chemistry of the University of Lausanne is now fully operational for 
sequence analysis tasks, and has received the name gcg.ch.embnet.org. All 
the accounts from the old machine at the EPFL have been transferred to the 
new one. Many thanks to the team at the Laboratoire de systemes logiques 
for their help over the last year!

The GCG software suite (version 9) is installed, as well as several useful 
public-domain programs. EGCG will be added as soon as version 9 is 
released. The recent EMBnet / 3eme cycle romand course in sequence analysis 
demonstrated the performance and stability of this machine. If you need an 
account, please send an E-mail to Claude Bonnard ( 
Claude.Bonnard at isrec.unil.ch ). Note that only Swiss academic users 

Victor Jongeneel


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