A graph layout algorithm for drawing metabolic pathways

Moritz Y. Becker


MOTIVATION: A large amount of data on metabolic pathways

is available in databases. The ability to visualise the

complex data dynamically would be useful for building

more powerful research tools to access the databases.

Metabolic pathways are typically modelled as graphs in

which nodes represent chemical compounds, and edges

represent chemical reactions between compounds. Thus,

the problem of visualising pathways can be formulated as

a graph layout problem. Currently available visual interfaces

to biochemical databases either use static images

or cannot cope well with more complex, non-standard


RESULTS: This paper presents a new algorithm for drawing

pathways which uses a combination of circular, hierarchic

and force-directed graph layout algorithms to compute

positions of the graph elements representing main

compounds and reactions. The algorithm is particularly designed

for cyclic or partially cyclic pathways or for combinations

of complex pathways. It has been tested on five

sample pathways with promising results.


Publication typeArticle
Published inBioinformatics
PublisherOxford University Press
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