Abstract
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90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.
doi:10.1016/S1045-926X(03)00030-2 
Copyright © 2003 Elsevier Science Ltd. All rights reserved.
Visual comparison of metabolic pathways
Received 20 December 2002;
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Abstract
Biological databases contain a large amount of data about metabolic pathways, in particular about similar pathways in different species. Biologists are familiar with visual representations of metabolic pathways. Pathway diagrams help them to understand the complex relationships between the components of the pathways, to extract information from the data, and to compare pathways between different species. However, visual interfaces to metabolic pathway databases cannot cope well with the visual comparison of similar pathways in different species.
This paper presents a new approach for the visual comparison of metabolic pathways which uses a graph drawing algorithm. Using layout constraints, identical parts of similar pathways in different species are placed side by side, thereby highlighting similarities and differences between these pathways. This visualization method can be used as a visual interface to databases. It supports different layout styles and has been tested with data obtained from the BioPath system and the KEGG database.
Author Keywords: Metabolic pathways; Pathway comparison; Visualization; Graph drawing; Constraints
