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Call for prior art on Patent 5,764,992

From: Reinhard Schneider <reinhard.schneider@embl.de>
Date: Thu, 18 Jun 2009 16:52:27 +0200
Message-Id: <7842D80E-FAFE-417B-AFC0-767CD0AB6DAF@embl.de>
To: public-widgets-pag@w3.org
Dear PAG-Team,

please find attached some documents which describe an automated  
sequence analysis system for biological DNA and protein sequences.
The system had an automatic update procedure (db_update)  for the  
underlying databases. It performed the updates automatically and  
triggered a range of actions like reformatting, indexing and updating  
depended system tools.

The first publication of the system appeared 1994 (see reference below).

I also attach a more detailed description of the system  
(genequiz.html) and a kind of help file for the update script itself  
(update.rtf). This software was
later part of a commercial package and the further development is  
still in use.

I hope this is of any help and feel free to require more information.

Best regards,
Reinhard Schneider
Dr. Reinhard Schneider
Data Integration and Knowledge Management Group
European Molecular Biology Laboratory (EMBL)
69117 Heidelberg
Meyerhofstr. 1


GeneQuiz: a workbench for sequence analysis.

Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A.,  
Ouzounis, C., Sander, C.

Protein Design Group, European Molecular Biology Laboratory,  
Heidelberg, Germany.

Proceedings / . International Conference on Intelligent Systems for  
Molecular Biology ; ISMB. International Conference on Intelligent  
Systems for Molecular Biology

Volume 2, 1994, Pages 348-353


We present the prototype of a software system, called GeneQuiz, for  
large-scale biological sequence analysis. The system was designed to  
meet the needs that arise in computational sequence analysis and our  
past experience with the analysis of 171 protein sequences of yeast  
chromosome III. We explain the cognitive challenges associated with  
this particular research activity and present our model of the  
sequence analysis process. The prototype system consists of two parts:  
(i) the database update and search system (driven by perl programs and  
rdb, a simple relational database engine also written in perl) and  
(ii) the visualization and browsing system (developed under C++/ET++).  
The principal design requirement for the first part was the complete  
automation of all repetitive actions: database updates, efficient  
sequence similarity searches and sampling of results in a uniform  
fashion. The user is then presented with "hit-lists" that summarize  
the results from heterogeneous database searches. The expert's primary  
task now simply becomes the further analysis of the candidate entries,  
where the problem is to extract adequate information about functional  
characteristics of the query protein rapidly. This second task is  
tremendously accelerated by a simple combination of the heterogeneous  
output into uniform relational tables and the provision of browsing  
mechanisms that give access to database records, sequence entries and  
alignment views. Indexing of molecular sequence databases provides  
fast retrieval of individual entries with the use of unique  
identifiers as well as browsing through databases using pre-existing  
cross-references. The presentation here covers an overview of the  
architecture of the system prototype and our experiences on its  
applicability in sequence analysis.(ABSTRACT TRUNCATED AT 250 WORDS)
Received on Monday, 22 June 2009 08:56:07 UTC

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