TY - GEN A1 - Dittel, Agnes A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Polyhedral Aspects of Self-Avoiding Walks N2 - In this paper, we study self-avoiding walks of a given length on a graph. We consider a formulation of this problem as a binary linear program. We analyze the polyhedral structure of the underlying polytope and describe valid inequalities. Proofs for their facial properties for certain special cases are given. In a variation of this problem one is interested in optimal configurations, where an energy function measures the benefit if certain path elements are placed on adjacent vertices of the graph. The most prominent application of this problem is the protein folding problem in biochemistry. On a set of selected instances, we demonstrate the computational merits of our approach. T3 - ZIB-Report - 11-11 KW - Polyhedral Combinatorics KW - Integer Programming KW - Self-Avoiding Path KW - Protein Folding Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12576 ER - TY - GEN A1 - May, Patrick A1 - Bauer, Markus A1 - Köberle, Christian A1 - Klau, Gunnar T1 - A computational approach to microRNA detection N2 - During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures. T3 - ZIB-Report - 06-44 KW - microRNA Smith-Waterman RNA folding Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9383 ER -