GeneQuiz: A Workbench for Sequence Analysis

Wepresent the prototype of a software system, cMledGeneQuiz,for large-scale biological sequence analysis. The system was designed to meet the needs that arise in computational sequenceanalysis and our past experience with the analysis of 171protein sequencesof yeast chromosomeIII. Weexplain the cognitive chMlenges associated with this particular research activity and present, our modelof the sequenceanalysis process. Theprototype system consists of two parts: (i) the database updateand search system (driven by perl programsand rdb, a simplerelational database engine also written in perl) and (ii) the visualization and browsingsystem(developed under C++/ET++).The principal design requirement for the first paxt wasthe complete automationof all repetitive actions: databaseupdates, efficient sequencesimilarity searches and sampling of results in a uniform fashion. Thc user is then presented with "hit-lists" that summarize the results from heterogeneous database searches. The exp...

• Type: Conference
• Year: 1994
• Where: ISMB
• Authors: Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
• Keywords: Biological Sequence Analysis, Computational Biology, Heterogeneous Database Searches, ISMB 1994, Sequencesof Yeast ChromosomeIII