Lecture Notes in Bioinformatics 4643

Transcription

1 Lecture Notes in Bioinformatics 4643 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

2 Marie-France Sagot Maria Emilia M. T. Walter (Eds.) Advances in Bioinformatics and Computational Biology Second Brazilian Symposium on Bioinformatics, BSB 2007 Angra dos Reis, Brazil, August 29-31, 2007 Proceedings 13

3 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 Marie-France Sagot INRIA Rhône-Alpes, UMR 5558 Biométrie et Biologie Évolutive Université Claude Bernard, Lyon I 43, Bd du 11 novembre 1918, Villeurbanne cedex, France [email protected] Maria Emilia M. T. Walter Universidade de Brasília, Instituto de Ciências Exatas Departamento de Ciência da Computação (CIC) Campus Universitário Asa Norte, Brasília, DF, CEP: , Brazil [email protected] Library of Congress Control Number: CR Subject Classification (1998): H.2.8, F.2.1, I.2, G.2.2, J.2, J.3, E.1 LNCS Sublibrary: SL 8 Bioinformatics ISSN ISBN Springer Berlin Heidelberg New York ISBN Springer Berlin Heidelberg New York 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. Springer is a part of Springer Science+Business Media springer.com Springer-Verlag Berlin Heidelberg 2007 Printed in Germany Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper SPIN: /

4 Preface The Brazilian Symposium on Bioinformatics (BSB 2007) was held in Angra dos Reis (Rio de Janeiro), Brazil, August 29-31, 2007, at the Portogalo Suite Hotel. BSB 2007 was the second BSB symposium, although BSB is a new name for the Brazilian Workshop on Bioinformatics (WOB). This previous event had three consecutive editions in 2002 (Gramado, Rio Grande do Sul), 2003 (Macaé, Rio de Janeiro), and 2004 (Brasilia, Distrito Federal). The change from workshop to symposium reflects the increased quality and interest of the meeting. BSB 2007 was co-located with the International Workshop on Genomic Databases (IWGD 2007). For BSB 2007, we had 60 submissions: 36 full papers and 24 extended abstracts, submitted to two tracks, computational biology/bioinformatics and applications. The second track was created in order to receive and discuss research work with a biological approach, and so to reinforce the participation of biologists in the event. These proceedings contain 13 full papers that were accepted, plus 6 extended abstracts. These papers and abstracts were carefully refereed and selected by an international Program Committee of 48 members, with the help of some additional reviewers, all listed on the following pages. We believe that this volume represents a fine contribution to current research in computational biology and bioinformatics, as well as in molecular biology. The editors would like to thank: the authors, for submitting their work to the symposium, and the invited speakers Roded Sharan (Tel-Aviv University, Israel), Alberto Martín Rivera Dávila (Fundação Oswaldo Cruz, and João Paulo Kitajima (Allelyx Applied Genomics, ; the Program Committee members and the other reviewers for their support in the review process; the General Chair Sérgio Lifschitz and the local organizers Daniel Xavier de Sousa, Cristian Tristão and José Maria Monteiro; the symposium sponsors (see list in this volume); Nalvo Franco de Almeida Jr., João Carlos Setubal, José Carlos Mombach, Marcelo de Macedo Brígido, and again Sérgio Lifschitz, members of the Brazilian Computer Societys (SBC) special committee for computational biology; and Springer for agreeing to print this volume. August 2007 Marie-France Sagot Maria Emilia M. T. Walter

5 Organization BSB 2007 was organized by the department of Informatics - Pontifical Catholic University of Rio de Janeiro/Brazil. Executive Committee Conference Chair Local Arrangements Sérgio Lifschitz Pontifical Catholic University of Rio de Janeiro Brazil Daniel Xavier de Sousa Cristian Tristao Jose Maria Monteiro Pontifical Catholic University of Rio de Janeiro Brazil Scientific Program Committee Program Chairs Marie-France Sagot INRIA, France Computational Biology and Bioinformatics Maria Emilia Machado Telles Walter University of Brasilia, Brazil Applications Program Committee Said S. Adi (Federal University of Mato Grosso do Sul, Nalvo F. Almeida (Federal University of Mato Grosso do Sul, Alberto Apostolico (Accademia Nazionale dei Lincei and Georgia Tech) Fernanda Baiao (UNIRIO, Valmir C. Barbosa (Federal University of Rio de Janeiro, Ana Lúcia Bazzan (Federal University of Rio Grande do Sul, Marcelo M. Brígido (University of Brasilia, Edson N. Cáceres (Federal University of Mato Grosso do Sul, André P.L.F.deCarvalho(UniversityofSão Paulo-São Carlos, Maria Cláudia Cavalcanti (Military Institute of Engineering, Dominique Cellier (University of Rouen, France)

6 VIII Organization Laurent Dardenne Alberto M. R. Dávila Zanoni Dias Carlos E. Ferreira Ana T. Freitas Richard Garrat Raffaele Giancarlo Katia S. Guimarães David Huson João P. Kitajima Gunnar Klau Gad Landau Melissa Lemos Natalia Martins Wellington Martins Marta Mattoso Alba C. M. A. Melo Antonio B. Miranda Satoru Miyano José C. Mombach Nadia Pisanti Alexandre Plastino Leila Ribeiro David Sankoff Luiz F. Seibel João C. Setubal Roded Sharan David Sherman Siang W. Song Marcílio C. P. de Souto Osmar Norberto de Souza Guilherme P. Telles Cristina Vieira Sérgio Verjovski-Almeida Martin Vingron Michael Waterman Fernando von Zuben (National Laboratory of Scientific Computation, (Fiocruz, (University of Campinas, (University of São Paulo, (Technical University of Lisbon, Portugal) (University of São Paulo-São Carlos, (Universita degli Studi di Palermo, Italy) (NCBI, USA/ Federal University of Pernambuco, (University of Tübingen, Germany) (Alellyx, (Freie Universität Berlin, Germany) (University of Haifa, Israel) (Pontifical Catholic University of Rio de Janeiro, (Embrapa/Biological Resources and Biotechnology, (Catholic University of Goias, (Federal University of Rio de Janeiro, (University of Brasilia, (Fiocruz, (The University of Tokyo, Japan) (Federal University of Santa Maria, (University of Pisa, Italy) (Federal Fluminense University, (Federal University of Rio Grande do Sul, (University of Ottawa, Canada) (Pontifical Catholic University of Rio de Janeiro, (Virginia Bioinformatics Institute, USA) (Tel-Aviv University, Israel) (CNRS, France) (University of São Paulo, (Federal University of Rio Grande do Norte, (Pontifical Catholic University of Rio Grande do Sul, (University of São Paulo-São Carlos, (INRIA, France) (University of São Paulo, (Max Planck Institute, Germany) (University of Southern California, USA) (University of Campinas,

7 Organization IX Additional Reviewers Christian Baudet Markus Bauer Luciano Digiampietri Alan Mitchell Durham Cristina G. Fernandes Ivan Gesteira Costa Filho Alexandre Paulo Francisco Ronaldo Fumio Hashimoto Dennis Kostka Alair Pereira do Lago Helena Cristina Gama Leitão Ana Carolina Lorena Simone de Lima Martins Mariá Cristina Vasconcelos Nascimento Christian Rausch Christine Steinhoff Yoshiko Wakabayashi Sponsoring Institutions Brazilian Computer Society CAPES

8 Table of Contents Selected Articles Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows... 1 K.S. Machado, E.K. Schroeder, D.D. Ruiz, and O. Norberto de Souza Gene Set Enrichment Analysis Using Non-parametric Scores Ariel E. Bayá, Mónica G. Larese, Pablo M. Granitto, Juan Carlos Gómez, and Elizabeth Tapia Comparison of Simple Encoding Schemes in GA s for the Motif Finding Problem: Preliminary Results Giovanna Martínez-Arellano and Carlos A. Brizuela Multi-Objective Clustering Ensemble with Prior Knowledge Katti Faceli, André C.P.L.F. de Carvalho, and Marcílio C.P. de Souto Biological Sequence Comparison Application in Heterogeneous Environments with Dynamic Programming Algorithms MarceloN.P.SantanaandAlbaCristinaM.A.Melo New EST Trimming Procedure Applied to SUCEST Sequences Christian Baudet and Zanoni Dias A Method for Inferring Biological Functions Using Homologous Genes Among Three Genomes Daniel A.S. Anjos, Gustavo G. Zerlotini, Guilherme A. Pinto, Maria Emilia M.T. Walter, Marcelo M. Brigido, Guilherme P. Telles, Carlos Juliano M. Viana, and Nalvo F. Almeida Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information Ivan G. Costa, Marcilio C.P. de Souto, and Alexander Schliep An Optimized Distance Function for Comparison of Protein Binding Sites Gábor Iván Comparing RNA Structures: Towards an Intermediate Model Between the Edit and the Lapcs Problems Guillaume Blin, Guillaume Fertin, Gaël Herry, and Stéphane Vialette

9 XII Table of Contents Evolving Phylogenetic Trees: A Multiobjective Approach Guilherme P. Coelho, Ana Estela A. da Silva, and Fernando J. Von Zuben Comparing Several Approaches for Hierarchical Classification of Proteins with Decision Trees Eduardo P. Costa, Ana C. Lorena, André C.P.L.F. Carvalho, Alex A. Freitas, and Nicholas Holden High Efficiency on Prediction of Translation Initiation Site (TIS) of RefSeq Sequences Cristiane N. Nobre, J. Miguel Ortega, and Antônio de Pádua Braga Extended Abstracts Outlining a Strategy for Screening Non-coding RNAs on a Transcriptome Through Support Vector Machines Roberto T. Arrial, Roberto C. Togawa, and Marcelo de M. Brígido Mapping Contigs onto Reference Genomes Nalvo F. Almeida, André C. Lima, Said S. Adi, Carlos J.M. Viana, Marcel Y. Nakazaki, Andrey A. Tamura, Luciana Y. Hiratsuka, and Leandro P. Brazil Molecular Dynamics Simulations of Cruzipains 1 and 2 at Different Temperatures Priscila V.S.Z. Capriles and Laurent E. Dardenne Genetic Algorithm for Finding Multiple Low Energy Conformations of Poly Alanine Sequences Under an Atomistic Protein Model Fábio L. Custódio, Hélio J.C. Barbosa, and Laurent E. Dardenne Cellular Fingerprints: A Novel Concept for the Integration of Experimental Data and Compound-Target-Pathway Relations Stefan Gunther, Stefanie Neumann, Jessica Ahmed, and Robert Preissner Identification of the Putative Class 3 R Genes in Coffea arabica from CafEST Database Magnólia A. Campos, Flávia B. Silva, Marilia S. Silva, Érika E.V.S. Albuquerque, Alexandre M. do Amaral, Cristiane C. Teixeira, Ângela Mehta, and Maria Fátima G. Sá Author Index