RUSSIAN ACADEMY OF SCIENCES SIBERIAN BRANCH INSTITUTE OF CYTOLOGY AND GENETICS THE SIXTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE Abstracts BGRS’2008 Novosibirsk, Russia June 22—28, 2008 Novosibirsk 2008 1 INTERNATIONAL PROGRAM COMMITTEE* Nikolay Kolchanov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia (Chairman of the Conference) Ralf Hofestadt University of Bielefeld, Germany (Co-Chairman of the Conference) Dagmara Furman Institute of Cytology and Genetics SB RAS, Novosibirsk, (Conference Scientific Secretary) Dmitry Afonnikov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Shandar Ahmad National Institute of Biomedical Innovation, Japan Philip Bourne University of California San Diego, San-Diego, USA Samir Brahmachari Institute of Genomics and Integrative Biology, Delhi, India Ming Chen Department of Bioinformatics Zhejiang University, Hangzhou, China А. Fazel Famili University of Ottawa, IIT/ITI - National Research Council Canada, Ottawa, Canada Mikhail Gelfand Institute for Information Transmission Problems RAS, Russia Boris M. Glinsky Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia Nikolay Goncharov Institute of Cytology and Genetics, Novosibirsk, Russia Charlie Hodgman Multidisciplinary Centre for Integrative Biology, School of Biosciences, University of Nottingham, UK Alexis Ivanov Institute of Biomedical Chemistry RAMS, Moscow, Russia Manfred Kayser Erasmus University Medical Centre Rotterdam, Rotterdam, The Netherlands Alexey Kochetov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Fyodor Kondrashov Division of Biological Sciences, University of California at San Diego, USA Jun-ichi Kudoh Center for Northeast Asian Studies, Tohoku University, Japan Vladimir Kuznetsov Division of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore Mikhail Lavrentiev Sobolev Institute of Mathematics, Institute of Automation and Electrometry, Novosibirsk, Russia Sergei Lukaschuk Hull Institute for Mathematical Science and Applications, The University of Hull, UK Luciano Milanesi National Research Council - Institute of Biomedical Technology, Italy Kenji Mizuguchi Bioinformatics and Computational Biology Group at the NiBio, The National Institute of Biomedical Innovation, Japan Mikhail Moshkin Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Vladimir Poroikov Laboratory for Structure-Function Based Drug Design, Institute of Biomedical Chemistry of RAMS, Moscow, Russia Jagath Rajapakse School of Computer Engineering, Nanyang Technological University, Singapore Igor Rogozin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA Nikolay Rubtsov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Maria Samsonova St.Petersburg State Polytechnic University, St.Petersburg, Russia Akinori Sarai Kyushu Institute of Technology (KIT), Iizuka, Japan Konstantin Skryabin “Bioingineering” Center, RAS, Russia Natalia Sournina Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Evgenii Vereshagin Siberian Center of pharmacology and biotechnology, Novosibirsk, Russia Evgenii Vityaev Sobolev Institute of Mathematics, Novosibirsk, Russia Valentin Vlassov Institute of Сhemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia Lev Zhivotovsky Institute of General Genetics RAS, Moscow, Russia LOCAL ORGANIZING COMMITTEE Ilya Akberdin Institute of Cytology and Genetics, Novosibirsk, Russia (Chairperson) Kirill Bezmaternykh Institute of Cytology and Genetics, Novosibirsk, Russia Ekaterina Denisova Institute of Cytology and Genetics, Novosibirsk, Russia Luba Glebova Institute of Cytology and Genetics, Novosibirsk, Russia Nadezda Glebova Institute of Cytology and Genetics, Novosibirsk, Russia Tatyana Karamisheva Institute of Cytology and Genetics, Novosibirsk, Russia Andrey Kharkevich Institute of Cytology and Genetics, Novosibirsk, Russia Galina Kiseleva Institute of Cytology and Genetics, Novosibirsk, Russia Sergey Lavryushev Institute of Cytology and Genetics, Novosibirsk, Russia Anna Onchukova Institute of Cytology and Genetics, Novosibirsk, Russia Svetlana Zubova Institute of Cytology and Genetics, Novosibirsk, Russia ISBN 978-5-91291-005-0 © Institute of Cytology and Genetics SB RAS, 2008 2 Organizers Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences Siberian Branch of the Russian Academy of Sciences The Vavilov Society of Geneticists and Breeders Laboratory of Theoretical Genetics Novosibirsk State University Chair of Information Biology PBSoft Ltd. Institute of Computational Technologies Sponsors Russian Foundation for Basic Research Carl Zeiss Bio-Rad Scientific Professional Equipment Siberian Branch of the Russian Academy of Sciences Federal Agency for Science and Innovation Hewlett Packard HTLabAG 3 Sections of the Conference 1. Genomics & Transcriptomics 2. Proteomics 3. Computational Systems Biology 4. Evolutionary and Population Computational Biology 5. Intelligence Data Analysis and Pattern Recognition in Bioinformatics 6. Bioinformatics and New Pharmacology 7. Computer Analysis and Image Recognition in Systems Biology 8. High-Performance Computing in Bioinformatics 9. Nanobioengineering 10. Microsymposium “Genetic Collections and Biodiversity of Cultivated Plants: Producing, Preservation and Cryoconservation” 11. First Micro-Satellite Symposium “Genetic Models in Postgenomic Biology” Abstracts have been printed without editing as received from the authors 4 Contents COMPARISON ANALYSING OF MUTANT GENE cbn1 WITH MUTANT GENE cao AND MOLECULAR MAPPING OF CAO GENE IN CHLAMYDOMONAS REINHARDTII Abdulla H., Mijit Gh., Xu qin, Rahman E., Chunaev A.S. ........................................................ 21 SUPERVISED LEARNING APPROACH TO IMPROVE ERROR PROBABILITIES FOR SHORT READ DNA SEQUENCING Abnizova I., Whiteford N., Skelly T., Brown C......................................................................... 22 MATHEMATICAL MODEL OF AUXIN METABOLISM IN SHOOTS OF ARABIDOPSIS THALIANA L Akberdin I.R., Omelyanchuk N.A., Fadeev S.I., Efimov V.M., Gainova I.A., Likhoshvai V.A. ................................................................................................. 23 OPENMP+MPI PARALLEL IMPLEMENTATION OF THE “MOLKERN” MOLECULAR MODELLING SOFTWARE PACKAGE Alemasov N.A., Fomin E.S........................................................................................................ 24 FUNCTIONAL ANNOTATION OF AMINO ACID SEQUENCES USING THE LOCAL SIMILARITY Alexandrov K.E., Sobolev B.N., Filimonov D.A., Poroikov V.V. ............................................ 25 SYSTEMS BIOLOGY STUDIES OF THE EFFECTS OF LEPTIN REPLACEMENT ON HUMAN GLUCOSE HOMEOSTASIS Andreev V.P , Paz-Filho G., Wong M-L., Licinio J................................................................... 26 HIV-1 GP120 V3-LOOP COMPARATIVE STRUCTURE ANALYSIS: SEARCH FOR THE STRUCTURALLY CONSERVED REGIONS Anishchenko I.V. ....................................................................................................................... 27 TEpredict: SOFTWARE FOR PREDICTING T-CELL EPITOPES Antonets D.V., Maksyutov A.Z. ................................................................................................ 28 DEVELOPMENT OF THE COMPUTER PROGRAM FOR DEFINING LEAF HAIRINESS IN WHEAT BASED ON ITS MICROSCOPE IMAGE PROCESSING Arsenina S.I., Afonnikov D.A., Pshenichnikova T.A. ............................................................... 29 NESTED GENES AND THE EVOLUTION OF METAZOAN GENOME ORGANIZATIONAL COMPLEXITY Assis R., Kondrashov A.S., Koonin E.V., Kondrashov F.A. ..................................................... 30 A BAYESIAN APPROACH TO EVOLUTIONARY HISTORY OF THE FAMILY POXVIRIDAE Babkin I.V., Shchelkunov S.N................................................................................................... 31 ACCELERATED ADAPTIVE EVOLUTION ON A NEWLY FORMED X CHROMOSOME Bachtrog D., Jensen J.D., Zhang Z............................................................................................. 32 ANALYSIS OF THE EVOLUTIONARY SPECIFICITIES OF THE YFIA И YHBH E. COLI GENES AND THEIR REGULATORY REGIONS Baryshev P.S., Oschepkov D.Yu., Khebodarova T.M., Afonnikov D.A. .................................. 33 A MORPHOMECHANICAL APPROACH TO DEVELOPMENT Beloussov L.V............................................................................................................................ 34 5 COMPUTATIONAL PIPELINE FOR SMALL RNA DISCOVERY AND EXPRESSION PROFILING BY NEXT GENERATION SEQUENCING Berezikov E., Cuppen E............................................................................................................. 35 MODELING EVOLUTION OF GENETIC REGULATION IN ARTIFICIAL ORGANISMS Beslon G., Sanchez-Dehesa Y., Peña J.-М. ............................................................................... 36 ANALYSIS OF A LIGHT ENTRAINMENT ON THE MATHEMATICAL MODEL OF MAMMALIAN CIRCADIAN OSCILLATOR Bezmaternykh K.D., Podkolodnaya O.A., Likhoshvai V.A....................................................... 37 USING SVM AND A MEASURE OF MOTIF ‘SURPRISE’ TO DISTINGUISH REGULATORY DNA Boekhorst R., Abnizova I., Naumenko F., Wernisch L.............................................................. 38 PREDICTION OF PROTEIN ALLERGENICITY BASED ON PROTEIN 3D STRUCTURE PROPERTIES Bragin A.O., Yarkova E.E., Demenkov P.S., Ivanisenko V.A..................................................