Gesellschaft für Informatik (GI) GI-Edition publishes this series in order to make available to a broad public recent findings in informatics (i.e. computer science and informa- Lecture Notes tion systems), to document conferences that are organized in co- operation with GI and to publish the annual GI Award dissertation. in Informatics Broken down into the fields of • Seminars • Proceedings • Dissertations • Thematics Ivo Grosse, Steffen Neumann, current topics are dealt with from the fields of research and Stefan Posch, Falk Schreiber, development, teaching and further training in theory and practice. The Editorial Committee uses an intensive review process in order Peter Stadler (Eds.) to ensure the high level of the contributions. The volumes are published in German or English. Information: http://www.gi-ev.de/service/publikationen/lni/ German Conference on Bioinformatics 2009 28th to 30th September 2009 Martin Luther University I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (eds): GCB 2009 Stadler (eds): P. Schreiber, F. Posch, S. Neumann, S. Grosse, I. Halle-Wittenberg, Germany ISSN 1617-5468 ISBN 978-3-88579-251-2 This volume contains the papers presented at the German Conference on Bioinfor- matics, GCB 2009, held in Halle (Saale), September 28-30, 2009. GCB is an annual international conference providing a forum for the presentation of research in 157 Proceedings Bioinformatics and Computational Biology. The conference is organized on behalf of the FG “Informatik in den Biowissenschaften (BIOINF)” of the German Society of Computer Science (GI), the AG “Computereinsatz in den Biowissenschaften” of the German Society of Chemical Technique and Biotechnology (DECHEMA) and the Studiengruppe “Bioinformatik” of the German Society for Biological Chemistry and Molecular Biology (GBM). IvoGrosse, Steffen Neumann, Stefan Posch, Falk Schreiber and Peter Stadler (Editors) German ConferenceonBioinformatics 2009 28th to 30th September2009 Martin Luther UniversityHalle-Wittenberg, Germany Gesellschaft f¨ur Informatik2009 Lecture Notes in Informatics (LNI) -Proceedings Series of the German Informatics society(GI) Volume P-157 ISBN 978-32-88579-251 -2 ISSN 1617-5468 Volume Editors Prof. Dr. IvoGroße MartinLuther UniversityHalle-Wittenberg, Germany Email: [email protected] Dr. SteffenNeumann Leibniz-Instituts f¨ur Pflanzenbiochemie (IPB) Halle, Germany Email: steff[email protected] Prof. Dr. Stefan Posch Martin Luther UniversityHalle-Wittenberg, Germany Email: [email protected] Prof.Dr. Falk Schreiber Martin Luther UniversityHalle-Wittenberg, Germanysowie Leibniz-Institut f¨ur Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Germany Email: [email protected] Prof. Dr. Peter F. Stadler Universit¨atLeipzig, Germany Email: [email protected] Series Editorial Board HeinrichC.Mayr, Universit¨atKlagenfurt, Austria (Chairman, mayr@ifit.uni-klu.ac.at) HinrichBonin, Leuphana-Universit¨at L¨uneburg, Germany Dieter Fellner, Technische Universit¨atDarmstadt, Germany UlrichFlegel, SAP Research, Germany UlrichFrank, Universit¨atDuisburg-Essen, Germany Johann-ChristophFreytag, Humboldt-Universit¨atBerlin, Germany Thomas Roth-Berghofer, DFKI Michael Goedicke,Universit¨atDuisburg-Essen Ralf Hofest¨adt,Universit¨atBielefeld Michael Koch,Universit¨atder Bundeswehr, M¨unchen, Germany Axel Lehmann, Universit¨atder Bundeswehr M¨unchen, Germany Ernst W. Mayr, Technische Universit¨at M¨unchen, Germany Sigrid Schubert, Universit¨atSiegen, Germany MartinWarnke, Leuphana-Universit¨at L¨uneburg, Germany Dissertations Dorothea Wagner, Universit¨atKarlsruhe, Germany Seminars Reinhard Wilhelm, Universit¨atdes Saarlandes, Germany Thematics Andreas Oberweis, Universit¨atKarlsruhe (TH) %c Gesellschaft f¨ur Informatik, Bonn 2009 printed by K¨ollenDruck+Verlag GmbH, Bonn Preface This volume containspaperspresented at the GermanConferenceonBioinformat- ics, GCB 2009,held in Halle (Saale), Germany, September28-30, 2009. The Ger- man ConferenceonBioinformatics is an annual, internationalconference, which provides aforumfor thepresentation of currentresearchinbioinformatics and computationalbiology.Itisorganized on behalf of the Special Interest Group on Informatics in Biologyofthe German SocietyofComputerScience (GI) and the German SocietyofChemical Technique and Biotechnology(Dechema) in coopera- tion with theGerman Societyfor Biochemistry and MolecularBiology (GBM). Six leading scientists were invited to givekeynote lectures to the conference. Svante P¨a¨abospoke on “A Neandertal PerspectiveonHuman Origins”, David Fell on “Building and Analyzing Genome-Scale Models of Metabolism”,and Ewan Birney on “Ensembl and ENCODE: Understanding our genome and its variation”. The focus of GCB 2009 —applying bioinformatics approaches to the field of plant science —isreflected in the keynotes“Phenotyping of Plants: Quantification of Structure and Function —Conceptsand Infrastructure” by UlrichSchurr and “Challenges of utilizing plantgenetic resources” by Andreas Graner.The lecture by Theo vanHintum on “The role of bioinformatics in aglobalattempttofight hunger” wasgiven open to the generalpublic. The scientific programcomprised 22 contributed talks presenting 18 regular and fourshort papers. These were selected from atotal of 47 submissions after review by the program committee All regularpapersand one short paper are collected in this proceedings. The remaining short papers and the 128poster abstractsaccepted to be presented at the poster session are published in aseparate volume. We liketothankall program committeemembers andall localorganizers and helpers for the efforts. Thanks are also due to all contributing to and participating in GCB 2009 and the sponsors for their financial support of the conference.Special thanks to Matthias H¨ubenthal for compiling these proceedings. August 2009,Ivo Große, Martin Luther UniversityHalle-Wittenberg Steffen Neumann, IPB Halle Stefan Posch, Martin Luther UniversityHalle-Wittenberg Falk Schreiber, UniversityofHalle-Wittenberg &IPK Gatersleben, Germany Peter F. Stadler,UniversityLeipzig Program committee Rolf Backofen ..................Albert-Ludwigs-UniversityFreiburg,Germany Sebastian B¨ocker..................Friedrich-Schiller-UniversityJena, Germany ThomasDandekar ..............UniversityofWuerzburg W¨urzburg, Germany Dirk Drasdo .............................INRIA Paris-Rocquencourt, France DmitrijFrishman...................Technical UniversityofMunich,Germany Georg Fuellen ............................UniversityofGreifswald, Germany Robert Giegerich.............................. Bielefeld University, Germany Jan Gorodkin ..........................UniversityofCopenhagen, Denmark IvoGroße.............Martin-Luther-UniversityofHalle-Wittenberg, Germany Arndt vonHaeseler...... Center for IntegrativeBioinformatics Vienna,Austria IvoHofacker................................. UniversityofVienna,Austria Dirk Holste .............................................. Vienna, Austria Janet Kelso............ MPI for Evolutionary Anthropology Leipzig, Germany Ina Koch ............Technical UniversityofApplied Sciences Berlin, Germany Oliver Kohlbacher ........................... Tuebingen University, Germany Jan Korbel...................................................New Haven Hans-Peter Lenhof................ Saarland UniversitySaarbr¨ucken, Germany Jens L´eon ................................................ Bonn, Germany David Marshall ..... Scottish Crop ResearchInstituteDundee, United Kingdom Irmtraud Meyer........................................ Vancouver, Canada Burkhard Morgenstern .................... UniversityofG¨o ttingen, Germany AxelMosig......................................... PICB Shanghai, China Vince Moulton ...........UniversityofEast Anglia Norwich,United Kingdom Steffen Neumann ....... Leibniz-Institutf¨u rPflanzenbiochemie Halle, Germany Sascha Ott..........................UniversityofWarwick,United Kingdom Yves vandePeer ................................GhentUniversity, Belgium Stefan Posch............Martin Luther UniversityHalle-Wittenberg, Germany Stephen Rudd .....................................................Turku UweScholz ..................................... IPK Gatersleben, Germany Dietmar Schomburg............Technische Universit¨atBraunschweig, Germany Falk Schreiber ........MLU Halle-Wittenberg Halle/IPK Gatersleben, Germany Michael Schr¨oder ................................... TU Dresden,Germany Stefan Schuster ................................ UniversityofJena, Germany Joachim Selbig ...............................UniversityPotsdam, Germany Korbinian Strimmer..........................UniversityofLeipzig, Germany Andrew Torda .............................UniversityofHamburg, Germany MartinVingron ................. MPI f¨ur molekulare GenetikBerlin,Germany Bernd Weisshaar .............................. Bielefeld University, Germany EdgarWingender ........................UniversityofGoettingen, Germany Ralf Zimmer ...................................... LMU Munich,Germany Supporting scientificsocieties Gesellschaftf¨u rBiochemie und Molekularbiologie e.V. (GBM) http://www.gbm-online.de/ Gesellschaft f¨ur Chemische Technik und Biotechnologie e.V. (DECHEMA) http://www.dechema.de/en/start_en.html Gesellschaft f¨ur Informatik e.V. (GI), Fachgruppe4.0.2 http://www.cebitec.uni-bielefeld.de/ groups/fg402/ Non-profit sponsors Leibniz Institute of PlantBiochemistry (IPB) Halle http://www.ipb-halle.de/ Leibniz Institute of PlantGenetics and Crop PlantResearch(IPK)Gatersleben