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BRAZILIAN SYMPOSIUM on BIOINFORMATICS August, 29 - 31, 2007 Angra Dos Reis – Rio De Janeiro Brasil

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BRAZILIAN SYMPOSIUM on BIOINFORMATICS August, 29 - 31, 2007 Angra Dos Reis – Rio De Janeiro Brasil BRAZILIAN SYMPOSIUM ON BIOINFORMATICS August, 29 - 31, 2007 Angra dos Reis – Rio de Janeiro Brasil BSB 2007 Poster Proceedings Conference Chair Sérgio Lifschtiz Department of Informatics - Pontificial Catholic University/Rio de Janeiro Brazil Volume Editors Marie-France Sagot – INRIA – France Maria Emília M. T. Walter – University of Brasília – Brazil Promotion Brazilian Computer Society – SBC Brazilian Symposium on Bioinformatics (2007 : Angra dos Reis, RJ) B827 BSB 2007 poster proceedings, August, 29-31, 2007, Angra dos Reis, Rio de Janeiro, Brasil / conference chair Sérgio Lifschtiz ; volume editors Marie-France Sagot, Maria Emília M. T. Walter. -- [Angra dos Reis] : Brazilian Computer Society, [2007]. 1 CD-ROM. ISBN 978-85-7669-123-5 1. Bioinformática – Congresso. I. Lifschtiz , Sérgio. II. Sagot, Marie-France. III. Walter, Maria Emília M. T. IV. Título. CDD21 004 CDD21 570 Preface The Brazilian Symposium on Bioinformatics (BSB 2007) was held in Angra dos Reis (Rio de Janeiro), Brazil, August 29-31, 2007, on the Portogalo Suite Hotel. It is an event promoted by the Brazilian Computer Society’s (SBC) special committee for computational biology (CEBioComp). BSB 2007 was the second BSB symposium, though BSB is a new name for a predecessor event called Brazilian Workshop on Bioinformatics (WOB). This previous event had three consecutive editions in 2002 (Gramado, Rio Grande do Sul), 2003 (Maca´e,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 held co-located with the International Workshop on Genomic Databases (IWGD 2007). For BSB 2007, we had 60 submissions: 36 full papers and 24 extended ab- stracts, submitted to two tracks, computational biology/bioinformatics and ap- plications. The second track was created in order to receive and discuss research works with a biological approach, and so to reinforce the participation of the bi- ologists on the event. From these, 13 full papers and 6 extended abstracts were selected to be published on the Lecture Notes on Bioinformatics (LNBI)/Lecture Notes on Computer Science (Springer-Verlag, Germany). These papers and ab- stracts were carefully refereed and selected by an international program com- mittee of 48 members, with the help of some additional reviewers, all of whom are listed on the following pages. But, as we received many interesting works that could not be included on the LNBI, we decided to create another volume containing these other selected works. We believe that this poster proceedings represents a good contribution to research in bioinformatics and computational biology, 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 Mart´ın Rivera D´avila (Funda¸c˜ao Oswaldo Cruz-Brazil) and Jo˜ao Paulo Kitajima (Allelyx Applied Genomics-Brazil); the program committee members and the other reviewers for their support in the review process; the general chair S´ergio Lifschitz and the local organizers Daniel Xavier de Sousa, Cristian Trist˜ao and Paulo Roberto Gomes; the symposium sponsors (see list in this volume); and Nalvo Franco de Almeida Jr., Jo˜ao Carlos Setubal, Jos´eCarlos Mombach, Marcelo de Macedo Br´ıgido, and again S´ergio Lifschitz, members of the CEBioComp. August 2007 Marie-France Sagot Maria Emilia M. T. Walter Organization BSB 2007 was organized by the Department of Informatics - Pontifical Catholic University of Rio de Janeiro/Brazil. Executive Committee Conference Chair: S´ergio Lifschitz Pontifical Catholic University of Rio de Janeiro Brazil Local Arrangements: Daniel Xavier de Sousa Cristian Trist˜ao Paulo Roberto Gomes 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 V Program Committee Said S. Adi (Federal University of Mato Grosso do Sul, Brazil) Nalvo F. Almeida (Federal University of Mato Grosso do Sul, Brazil) Alberto Apostolico (Accademia Nazionale dei Lincei and Georgia Tech) Fernanda Baiao (UNIRIO, Brazil) Valmir C. Barbosa (Federal University of Rio de Janeiro, Brazil) Ana L´ucia Bazzan (Federal University of Rio Grande do Sul, Brazil) Marcelo M. Br´ıgido (University of Brasilia, Brazil) Edson N. C´aceres (Federal University of Mato Grosso do Sul, Brazil) Andr´eP. L. F. de Carvalho (University of S˜ao Paulo-S˜ao Carlos, Brazil) Maria Cl´audia Cavalcanti (Military Institute of Engineering, Brazil) Dominique Cellier (University of Rouen, France) Laurent Dardenne (National Laboratory of Scientific Computation, Brazil) Alberto M. R. D´avila (Fiocruz, Brazil) Zanoni Dias (University of Campinas, Brazil) Carlos E. Ferreira (University of S˜ao Paulo, Brazil) Ana T. Freitas (Technical University of Lisbon, Portugal) Richard Garrat (University of S˜ao Paulo-S˜ao Carlos, Brazil) Raffaele Giancarlo (Universita degli Studi di Palermo, Italy) Katia S. Guimar˜aes (NCBI, USA/ Federal University of Pernambuco, Brazil) David Huson (University of Tubingen, Germany) Jo˜ao P. Kitajima (Alellyx, Brazil) Gunnar Klau (Freie Universitt Berlin, Germany) Gad Landau (University of Haifa, Israel) Melissa Lemos (Pontifical Catholic University of Rio de Janeiro, Brazil) Natalia Martins (Embrapa/Biological Resources and Biotechnology, Brazil) Wellington Martins (Catholic University of Goias, Brazil) Marta Mattoso (Federal University of Rio de Janeiro, Brazil) Alba C. M. A. Melo (University of Brasilia, Brazil) Antonio B. Miranda (Fiocruz, Brazil) Satoru Miyano (The University of Tokyo, Japan) Jos´eC. Mombach (Federal University of Santa Maria, Brazil) Nadia Pisanti (University of Pisa, Italy) Alexandre Plastino (Federal Fluminense University, Brazil) Leila Ribeiro (Federal University of Rio Grande do Sul, Brazil) David Sankoff (University of Ottawa, Canada) Luiz F. Seibel (Pontifical Catholic University of Rio de Janeiro, Brazil) Jo˜ao C. Setubal (Virginia Bioinformatics Institute, USA) Roded Sharan (Tel-Aviv University, Israel) David Sherman (CNRS, France) Siang W. Song (University of S˜ao Paulo, Brazil) Marc´ılio C. P. de Souto (Federal University of Rio Grande do Norte, Brazil) Osmar Norberto de Souza (Pontifical Catholic University of Rio Grande do Sul, Brazil) Guilherme P. Telles (University of S˜ao Paulo-S˜ao Carlos, Brazil) Cristina Vieira (INRIA, France) S´ergio Verjovski-Almeida (University of S˜ao Paulo, Brazil) Martin Vingron (Max Planck Institute, Germany) Michael Waterman (University of Southern California, USA) Fernando von Zuben (University of Campinas, Brazil) VI 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 Leit˜ao Ana Carolina Lorena Simone de Lima Martins Mari´aCristina Vasconcelos Nascimento Christian Rausch Christine Steinhoff Yoshiko Wakabayashi Sponsoring Institutions Brazilian Computer Society CAPES Special Committee for Computational Biology from the Brazilian Computer Society Nalvo Franco de Almeida Jr. Federal University of Mato Grosso do Sul - Brasil (coordinator) Jo˜ao Carlos Setubal Virginia Bioinformatics Institute - USA Jos´eCarlos Mombach Federal University of Santa Maria - Brasil Marcelo de Macedo Br´ıgido University of Bras´ılia - Brasil Maria Em´ılia M. T. Walter University of Bras´ılia - Brasil S´ergio Lifschitz Pontifical Catholic University of Rio de Janeiro - Brasil Table of Contents Selected works Impaired expression of NER gene network in sporadic solid tumors ...... 10 Mauro A. A. Castro, Jos´eC. M. Mombach, Rita M. C. de Almeida, Jos´eC. F. Moreira A tool for cluster number estimation in SOM-based gene expression pattern analysis................................................... 14 Elmer A. Fern´andez, M´onica Balzarini EGGview: VIsualization of EGG Comparative Data Using GBrowse ..... 24 Nalvo F. Almeida, Marcel Y. Nakazaki, Andrey A. Tamura, Luciana Y. Hiratsuka, Andr´eC. Lima, Said S. Adi, Carlos J.M. Viana, Leandro P. Brazil Topological Indices and Graph Theory: a Useful Tool for the Characterization of Peptides? ....................................... 28 Alan Talevi, Carolina L. Bellera, Luis E. Bruno-Blanch Phthorimaea operculella granuloviruse: sequence analysis of 5 genes from, 16 geographical isolates ...................................... 40 Marc Sporleder, Octavio Zegarra Aliaga, Vilma Hualla Mamani, Reinhard Simon, Jrgen Kroschel Predicting Physicochemical Properties for Drug Design Using Clustering and Neural Network Learning ............................. 46 Axel J. Soto, Ignacio Ponzoni, Gustavo E. Vazquez Biota-RIO: a database of animal biodiversity in the State of Rio de Janeiro 58 Vin´ıcius Schmitz Pereira Nunes, Alexandre Rossi Paschoal, Clarice Augusta Carvalho Cardoso, Ana Tereza Ribeiro Vasconcelos, Cl´audia Augusta de Moraes Russo A Genetic Algorithm for Detection of Relevant Descriptors in ADMET Prediction ................................................... .... 62 Rocio L. Cecchini, Axel J. Soto, Gustavo E. Vazquez, Ignacio Ponzoni A Distributed Algorithm for Phylogenetics Inference................... 66 Felipe Albrecht, Jomi Hubner, Alberto D´avila Phylogenetic analysis of the wrky transcription factors gene superfamily in coffee plants ..................................................
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