Affiliations: Technical University of Applied Sciences Berlin, FBV,
WG Bioinformatics, Seestr. 64, 13347 Berlin, Germany. Tel.: +49 (0)30 4504
3972; Fax: +49 (0)30 4504 3959; E-mail: {ina.koch,
markus.schueler}@tfh-berlin.de | Brandenburg University of Technology at Cottbus,
Department of Computer Science, 03013 Cottbus, Germany. Tel.: +49 (0)355 69
3884; Fax: +49 (0)355 69 3830; E-mail:
[email protected]
Note: [] Corresponding author
Abstract: To understand biochemical processes caused by, e.g., mutations or
deletions in the genome, the knowledge of possible alternative paths between
two arbitrary chemical compounds is of increasing interest for biotechnology,
pharmacology, medicine, and drug design. With the steadily increasing amount of
data from high-throughput experiments new biochemical networks can be
constructed and existing ones can be extended, which results in many large
metabolic, signal transduction, and gene regulatory networks. The search for
alternative paths within these complex and large networks can provide a huge
amount of solutions, which can not be handled manually. Moreover, not all of
the alternative paths are generally of interest. Therefore, we have developed
and implemented a method, which allows us to define constraints to reduce the
set of all structurally possible paths to the truly interesting path set. The
paper describes the search algorithm and the constraints definition language.
We give examples for path searches using this dedicated special language for a
Petri net model of the sucrose-to-starch breakdown in the potato tuber.
Availability: http://sanaga.tfh-berlin.de/~stepp/
Keywords: Petri nets, systems biology, biochemical networks, metabolic networks, signal transduction networks, path search with constraints, graph theory, sucrose-to-starch breakdown, potato tuber
