Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Exact Sketch-Based Read Mapping

Schulz T, Medvedev P. Exact Sketch-Based Read Mapping. In: Belazzougui D, Ouangraoua A, Schloss Dagstuhl – Leibniz-Zentrum für Informatik GmbH, eds. 23rd International Workshop on Algorithms in Bioinformatics. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023.Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a "similar sequence". Traditionally, "similar sequence" was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold. In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in {O}(|t| + |p| + ²) time and Θ(²) space, where |t| is the number of k-mers inside the sketch of the reference, |p| is the number of k-mers inside the read’s sketch and is the number of times that k-mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm’s performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2

SLIVAR needs models of interactional intelligence

Buschmeier H. SLIVAR needs models of interactional intelligence. In: Devillers L, Kawahara T, Moore RK, Scheutz M, Schloss Dagstuhl – Leibniz-Zentrum für Informatik, eds. Spoken Language Interaction with Virtual Agents and Robots (SLIVAR): Towards Effective and Ethical Interaction (Dagstuhl Seminar 20021). Dagstuhl Reports. Vol 10. Dagstuhl, Germany; 2020: 17–18

A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance

Bergeron A, Mixtacki J, Stoye J. A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. In: Apostolico A, Dress A, Parida L, Schloss Dagstuhl, Leibniz-Zentrum für Informatik, eds. Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings. Vol 10231. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany; 2010: Online-Ressource.The genomic distance problem in the Hannenhalli-Pevzner (HP) theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of translocations, fusions, fissions and inversions that transform one genome into the other. We will present a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way, and a linear-time algorithm for computing this distance