ADVANCED VISUALIZATION OF METABOLIC PATHWAYS IN PATHDB

National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, New Mexico 87505, USA

Metabolic pathways have traditionally been represented graphically as arrow diagrams. The arrows represent reactions and connect metabolites. Enzyme and metabolite names label the arrows and nodes; sometimes chemical structures of metabolites also are included. Usually one considers pathways in terms of the conversions of a specific chemical moiety (sugar in glycolysis) and the co-substrates that do not carry it (adenine nucleotides in glycolysis) are drawn in smaller characters on the sides of the arrows. Each co-substrate may appear in several places in the diagram, while the main metabolites are represented in a single location. Biochemists are comfortable interpreting these diagrams and so it is important that any software-based representation follow these conventions as closely as possible. PathDB, a metabolic Pathway database requires that pathways be drawn automatically because the goal is to allow users to make up pathways with any set of connected reactions, not just those that are traditionally represented in textbooks. Thus its visualization software, Pathway Viewer, must draw pathways automatically. One challenge is that metabolic pathways often contain simultaneously both cyclical and branched structures. While there are algorithms efficient for either one of these, we are aware of none that can deal with both in the same graph. We developed an algorithm that analyses the pathway structure and, depending on the connectivity of the reaction set, renders each cycle and branch optimally and then combines them in a diagram essentially like the classical pathway representations. Another important feature of this software is that it provides alternative views of each pathway and lets the user change these if desired. Pathway Viewer is demonstrated together with the rest of the PathDB database in a software session and a poster describes specific pathway diagrams produced with it.