We study the NP-hard List-Colored Graph Motif problem which, given an undirected list-colored graph G=(V,E) and a multiset M of colors, asks for maximum-cardinality sets S ? V and M? ? M such that G[S] is connected and contains exactly (with respect to multiplicity) the colors in M?. List-Colored Graph Motif has applications in the analysis of biological networks. We study List-Colored Graph Motif with respect to three different parameterizations. For the parameters motif size |M| and solution size |S|, we present fixed-parameter algorithms, whereas for the parameter |V|-|M|, we show W-hardness for general instances and achieve fixed-parameter tractability for a special case of List-Colored Graph Motif. We implemented the fixed-parameter algorithms for parameters |M|and |S|, developed further speed-up heuristics for these algorithms, and applied them in the context of querying protein-interaction networks, demonstrating their usefulness for realistic instances. Furthermore, we show that extending the request for motif connectedness to stronger demands, such as biconnectedness or bridge-connectedness leads to W-hard problems when the parameter is the motif size |M|.
|Number of pages||13|
|Journal||IEEE/ACM Transactions on Computational Biology and Bioinformatics|
|Publication status||Published - 2011|
Betzler, N., Van Bevern, R., Fellows, M., Komusiewicz, C., & Niedermeier, R. (2011). Parameterized Algorithmics for Finding Connected Motifs in Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(5), 1296-1308. https://doi.org/10.1109/TCBB.2011.19