Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.
BACKGROUND
In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites  , which are the minimal subsets of   that are able to produce all the metabolites in T. Such subsets are called the minimal precursor sets of T. The problem is then whether we can enumerate all of them efficiently.


RESULTS
We propose a new characterization of precursor sets as the inputs of reaction sets called factories and an efficient algorithm to decide if a set of sources is precursor set of T. We show proofs of hardness for the problems of finding a precursor set of minimum size and of enumerating all minimal precursor sets T. We propose two new algorithms which, despite the hardness of the enumeration problem, allow to enumerate all minimal precursor sets in networks with up to 1000 reactions.


BACKGROUND
Source code and datasets used in our benchmarks are freely available for download at http://sites.google.com/site/pitufosoftware/download.


BACKGROUND
vicente77@gmail.com, pvmilreu@gmail.com or marie-france.sagot@inria.fr.
Université de Lyon, F-69000 Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France. vicente77@gmail.com
Vicente
V
Acuña
Paulo Vieira
PV
Milreu
Ludovic
L
Cottret
Alberto
A
Marchetti-Spaccamela
Leen
L
Stougie
Marie-France
MF
Sagot
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D053858:Metabolic Networks and Pathways; D008962:Models, Theoretical