Paper Info
Title
GeneQuiz: a workbench for sequence analysis.
Abstract
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)
Year
Venue
Keywords
1994
ISMB
sequence analysis,rule based system,software systems,protein sequence
Field
DocType
Volume
Protein structure database,Relational database,Computer science,Search engine indexing,Software system,Artificial intelligence,Sequence profiling tool,Bioinformatics,Unique identifier,Machine learning,Perl,Sequence analysis
Conference
2
ISSN
Citations 
PageRank 
1553-0833
20
14.58
References 
Authors
2
7
Name
Order
Citations
PageRank
M Scharf12014.58
Reinhard Schneider 0002214938.04
G Casari36423.70
Peer Bork44451694.12
Alfonso Valencia52577322.43
Christos A. Ouzounis6879200.77
Chris Sander7469157.99