Bioinformatics Vol. 18 no. 90002 2002
Pages S219-S230
© 2002 Oxford University Press
BioMiner—modeling, analyzing, and visualizing biochemical pathways and networks
irava 1
1 Center for Bioinformatics, Saarland University,
P.O. Box 151150, Saarbrücken, 66041, Germany
2 Wilhelm-Schickard Institut für Informatik,
University of Tübingen, Sand 13, Tübingen, 72076, Germany
3 Umber, School of Biological Science,
University of Manchester, Manchester, M13 9PT, UK
Received on April 8, 2002
; accepted on June 15, 2002
Motivation: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet.
Results: We present a new software system—BioMiner—for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model—BioCore—which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms.
Availability: http://www.zbi.uni-saarland.de/chair/projects/BioMiner
Contact: schaefer{at}bioinf.uni-sb.de
Supplementary Information: Additional information on experimental results can be found on our web site.
Keywords: Biochemical data model, metabolic and regulatory pathways, visualization, Java, XML.
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