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Lecture Notes in Bioinformatics 6833 Edited by S. Istrail, P. Pevzner, and M. Waterman Editorial Board: A. Apostolico S. Brunak M. Gelfand T. Lengauer S. Miyano G. Myers M.-F. Sagot D. Sankoff R. Shamir T. Speed M. Vingron W. Wong Subseries of Lecture Notes in Computer Science Teresa M. Przytycka Marie-France Sagot (Eds.) Algorithms in Bioinformatics 11th International Workshop, WABI 2011 Saarbrücken, Germany, September 5-7, 2011 Proceedings 13 Series Editors Sorin Istrail, Brown University, Providence, RI, USA Pavel Pevzner, University of California, San Diego, CA, USA Michael Waterman, University of Southern California, Los Angeles, CA, USA Volume Editors Teresa M. Przytycka National Center for Biotechnology Information U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894, USA E-mail: [email protected] Marie-France Sagot Institut National de Recherche en Informatique et en Automatique (INRIA) and Université Lyon 1 (UCBL) 43 bd du 11 Novembre 1918, 69622 Villeurbanne cedex, France E-mail: [email protected] ISSN 0302-9743 e-ISSN 1611-3349 ISBN 978-3-642-23037-0 e-ISBN 978-3-642-23038-7 DOI 10.1007/978-3-642-23038-7 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2011934142 CR Subject Classification (1998): F.2, F.1, H.2.8, G.2, E.1, J.3 LNCS Sublibrary: SL 8 – Bioinformatics © Springer-Verlag Berlin Heidelberg 2011 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface We are pleased to present the proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI 2011) which took place in Saarbr¨ucken, Germany, September 5–7, 2011. The WABI 2011 workshop was part of the six ALGO 2011 conference meetings, which, in addition to WABI, included ESA, IPEC, WAOA, ALGOSENSORS, and ATMOS. WABI 2011 was hosted by the Max Planck Institute for Informatics, and sponsored by the European Association for Theoretical Computer Science (EATCS) and the International Society for Computational Biology (ISCB). See https://algo2011.mpi-inf.mpg.de/ for more details. The Workshop in Algorithms in Bioinformatics highlights research in al- gorithmic work for bioinformatics, computational biology, and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore direc- tions of future research. Original research papers (including significant work-in-progress) or state-of- the-art surveys were solicited for WABI 2011 in all aspects of algorithms in bioinformatics, computational biology, and systems biology. In response to our call, we received 77 submissions for papers and 30 were accepted. In addition, WABI 2011 hosted a distinguished lecture by Vincent Moulton, of the University of East Anglia, UK. We would like to sincerely thank the authors of all submitted papers and the conference participants. We also thank the Program Committee and their sub-referees for their hard work in reviewing and selecting papers for the workshop. We would especially like to thank Bernard Moret for all his advice and sup- port in carrying out the role of being Co-chairs, as well as EasyChair for making the management of the submissions to WABI such an easy process. Thanks once again to all who participated in making WABI such a success in 2011. For us it has been an exciting and rewarding experience. June 2011 Teresa Przytycka Marie-France Sagot Organization Program Committee Tatsuya Akutsu Kyoto University, Japan Jan Baumbach Max Planck Institute for Informatics, Germany Tanya Berger-Wolf UIC, USA Paola Bonizzoni Universit`a di Milano-Bicocca, Italy Dan Brown Cheriton School of Computer Science, University of Waterloo, Canada Michael Brudno University of Toronto, Canada Sebastian B¨ocker Friedrich Schiller University Jena, Germany Robert Castelo Universitat Pompeu Fabra, Spain Benny Chor School of Computer Science, Tel Aviv University, Israel Lenore Cowen Tufts University, USA Nadia El-Mabrouk University of Montreal, Canada Eleazar Eskin University of California, Los Angeles, USA Liliana Florea University of Maryland, USA Ana Teresa Freitas INESC-ID/IST, Technical University Lisbon, Portugal Anna Gambin Institute of Informatics, Warsaw University, Poland Olivier Gascuel LIRMM, CNRS - Universit´e Montpellier 2, France Raffaele Giancarlo Universit`adiPalermo,Italy Dan Gusfield UC Davis, USA Ivo Hofacker University of Vienna, Austria Barbara Holland University of Tasmania, Australia Daniel Huson University of T¨ubingen, Germany Igor Jurisica Ontario Cancer Institute, Canada Carl Kingsford University of Maryland, College Park, USA Gunnar Klau CWI, The Netherlands Mehmet Koyuturk Case Western Reserve University, USA Jens Lagergren SBC and CSC, KTH, Sweden Hans-Peter Lenhof Center for Bioinformatics, Saarland University, Germany Christine Leslie Memorial Sloan-Kettering Cancer Center, USA Stefano Lonardi UC Riverside, USA VIII Organization Ion Mandoiu University of Connecticut, USA Satoru Miyano Human Genome Center, Institute of Medical Science, University of Tokyo, Japan Bernard Moret EPFL, Switzerland Burkhard Morgenstern University of G¨ottingen, Germany Vincent Moulton University of East Anglia, UK Gene Myers HHMI Janelia Farm Research Campus, USA Itsik Pe’Er Columbia University, USA Nadia Pisanti Universit`a di Pisa, Italy Teresa Przytycka NCBI, NLM, NIH, USA Knut Reinert FU Berlin, Germany Juho Rousu University of Helsinki, Finland Yvan Saeys Flanders Institute for Biotechnology (VIB), Ghent University, Belgium Marie-France Sagot Universit´edeLyon,France Cenk Sahinalp Simon Fraser University, Canada David Sankoff University of Ottawa, Canada Thomas Schiex INRA, France Stefan Schuster LS Bioinformatik, Universit¨at Jena, Germany Russell Schwartz Carnegie Mellon University, USA Charles Semple Canterbury University, New Zealand Mona Singh Princeton University, USA Saurabh Sinha University of Illinois, USA Joerg Stelling ETH Zurich, Switzerland Leen Stougie Centrum voor Wiskunde en Informatica (CWI) and Technische Universiteit Eindhoven (TU/e), The Netherlands Jens Stoye Bielefeld University, Germany Michael Stumpf Imperial College London, UK Jerzy Tiuryn Warsaw University, Poland H´el`ene Touzet LIFL - CNRS, France Alfonso Valencia Spanish National Cancer Research Centre (CNIO), Spain Lusheng Wang University of Hong Kong City Chris Workman DTU, Denmark Alex Zelikovsky GSU, USA Louxin Zhang National University of Singapore Michal Ziv-Ukelson Ben Gurion University of the Negev, Israel Elena Zotenko Garvan Institute, Australia Additional Reviewers Agius, Phaedra Canzar, Stefan Al Seesi, Sahar Cho, DongYeon Andonov, Rumen Dao, Phuong Organization IX Degnan, James Mueller, Oliver Dehof, Anna Katharina Nicolae, Marius Della Vedova, Gianluca Pardi, Fabio Dondi, Riccardo Parrish, Nathaniel Doyon, Jean-Philippe Patro, Rob Duggal, Geet Pitk¨anen, Esa Duma, Denisa Polishko, Anton D¨orr, Daniel Roettger, Richard Ehrler, Carsten Rueckert, Ulrich El-Kebir, Mohammed Ruffalo, Matthew Erten, Sinan Russo, Lu´ıs Federico, Maria Rybinski, Mikolaj Fonseca, Paulo Salari, Raheleh Francisco, Alexandre Scheubert, Kerstin Frid, Yelena Schoenhuth, Alexander Gambin, Tomasz Scornavacca, Celine Gaspin, Christine Snir, Sagi Geraci, Filippo Startek, Michal Ghiurcuta, Cristina Stckel, Daniel Gorecki, Pawel Stevens, Kristian Harris, Elena Sun, Peng Hellmuth, Marc Swanson, Lucas Hoener Zu Siderdissen, Christian Swenson, Krister Hormozdiari, Farhad Szczurek, Ewa Huang, Yang Tantipathananandh, Chayant Hufsky, Franziska Taubert, Jan Ibragimov, Rashid Thapar, Vishal Jahn, Katharina Truss, Anke Kelk, Steven Ullah, Ikram Kennedy, Justin Weile, Jochen Kim, Yoo-Ah Willson, Stephen Lempel-Musa, Noa Winnenburg, Rainer Lin, Yu Winter, Sascha Lindsay, James Wittkop, Tobias Linz, Simone Wittler, Roland Lorenz, Ronny Wohlers, Inken Lynce, Ines Wolter, Katinka Malin, Justin Wu, Taoyang Manzini, Giovanni Wu, Yufeng Marschall, Tobias W´ojtowicz, Damian Menconi, Giulia Yorukoglu, Deniz Misra, Navodit Zaitlen, Noah Montangero, Manuela Zakov, Shay Mozes, Shay Zheng, Yu Table of Contents Automated Segmentation of DNA Sequences with Complex Evolutionary Histories ............................................ 1 Broˇna Brejov´a, Michal Burger, and Tom´aˇsVinaˇr Towards a Practical O(n log n) Phylogeny Algorithm ................ 14