MiS Preprint Repository

Delve into the future of research at MiS with our preprint repository. Our scientists are making groundbreaking discoveries and sharing their latest findings before they are published. Explore repository to stay up-to-date on the newest developments and breakthroughs.

MiS Preprint

Detecting Phylogenetic Footprint Clusters by Optimizing Barbeques

Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska and Peter F. Stadler


Taking a geometric view on a problem occurring in the context of phylogenetic footprinting, we study the so-called Best Barbeque Problem. The Best Barbeque Problem asks for simultaneously stabbing a maximum number of differently colored intervals from $K$ arrangements of colored intervals. This geometric problem leads to a combinatorial optimization problem, a decision version of which is shown to be NP-complete. Due to its relevance in biological applications, we propose two branch-and-bound algorithms to detect footprint clusters in some real world instances of phylogenetic footprints. Finally, we point out other geometric and combinatorial scenarios where optimizing barbeques might be of practical relevance.

Apr 18, 2005
Apr 18, 2005
phylogenetic footprint clusters, np-complete, best barbeque problem

Related publications

2005 Repository Open Access
Türker Biyikoglu, Peter F. Stadler, Sonja J. Prohaska and Axel Mosig

Detecting phylogenetic footprint clusters by optimizing barbeques