Advances in Bioinformatics and Computational Biology: 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012. Proceedings PDF
Preview Advances in Bioinformatics and Computational Biology: 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012. Proceedings
Lecture Notes in Bioinformatics 7409 EditedbyS.Istrail,P.Pevzner,andM.Waterman EditorialBoard: 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 Marcilio C.P. de Souto Maricel G. Kann (Eds.) Advances in Bioinformatics and Computational Biology 7th Brazilian Symposium on Bioinformatics, BSB 2012 Campo Grande, Brazil,August 15-17, 2012 Proceedings 1 3 SeriesEditors SorinIstrail,BrownUniversity,Providence,RI,USA PavelPevzner,UniversityofCalifornia,SanDiego,CA,USA MichaelWaterman,UniversityofSouthernCalifornia,LosAngeles,CA,USA VolumeEditors MarcilioC.P.deSouto UniversidadeFederaldePernambuco CentrodeInformática Recife,PE,Brazil E-mail:[email protected] MaricelG.Kann UniversityofMaryland/BaltimoreCounty DepartmentofBiologicalSciences Baltimore,MD,USA E-mail:[email protected] ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-642-31926-6 e-ISBN978-3-642-31927-3 DOI10.1007/978-3-642-31927-3 SpringerHeidelbergDordrechtLondonNewYork LibraryofCongressControlNumber:2012942078 CRSubjectClassification(1998):J.3,I.2,F.1,H.2.8,I.5,H.3 LNCSSublibrary:SL8–Bioinformatics ©Springer-VerlagBerlinHeidelberg2012 Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandthereforefreeforgeneraluse. Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface This volume contains the papers selected for presentation at BSB 2012:the 7th Brazilian Symposium on Bioinformatics held August 15–17, 2012, in Campo Grande (Mato Grosso do Sul), Brazil. The BSB is an international conference whichcoversallaspects ofbioinformatics andcomputationalbiology.The event isorganizedbythespecialinterestgroupinComputationalBiologyoftheBrazil- ian Computer Society (SBC). The BSB series started in 2005. In the period 2002–2004 its name was Brazilian Workshop on Bioinformatics (WOB). Thus, this year we celebrated the 10th anniversary. As in previous editions, BSB 2012had aninternationalProgramCommittee of 55 members. After a rigorous review process, 16 papers were accepted to be orallypresented.Allpaperswerereviewedbyatleastthreeindependentreview- ers.Thisyear,aselectionofthe acceptedpaperswasalsoinvitedforsubmission in expanded format to a special issue of the IEEE/ACM Transactions on Com- putational Biology and Bioinformatics (TCBB). We thank the IEEE/ACMand Marie-France Sagot, as editor-in-chief of the TCBB, for offering us this oppor- tunity. In addition to the technical presentations, BSB 2012 featured keynote talks. We are grateful to all of the invited speakers: Marcos V.G.B. da Silva (EMBRAPA, Brazil), Jos´e Fernando Garcia (UNESP, Brazil), Fernando D. Gonz´alez-Nilo (Universidad Andr´es Bello, Chile), Maricel G. Kann (University of Maryland/Baltimore,USA), and Jens Stoye (Bielefeld University, Germany). These proceedings also include a joint paper from two of the guest speakers. BSB 2012 was made possible by the dedication and work of many people and institutions, especially the Faculdade de Computac¸˜ao (Facom) of the Uni- versidade Federal do Mato Grosso do Sul (UFMS). We would like to express our sincere thanks to all Program Committee members, as well as to the ex- ternal reviewers, for their cooperation in the reviewing process. We appreciate their hard work that guaranteed the high quality of the technical program. We are also grateful to the local organizers, coordinated by Nalvo F. Almeida Jr. (Facom/UFMS, Brazil), and volunteers for their valuable help; the sponsors, in particular CNPq, CAPES and FUNDECT, for making the event financially vi- able;GuilhermeTellesforassistingwiththepreparationoftheproceedings;and Springer for agreeing to print this volume. Finally, we would like to thank the authors for their time and effort in sub- mittingtheirworktotheBSB2012,aswellastheattendees.Withoutthemthis event would not be possible. August 2012 Marcilio C.P. de Souto Maricel G. Kann Organization BSB 2012 was supported by the Brazilian Computer Society (SBC) and orga- nizedbyFaculdadede Computac¸˜aodaUniversidadeFederaldeMatoGrossodo Sul (UFMS); EmbrapaGado de Corte;Fundac¸˜ao de Apoio ao Desenvolvimento do Ensino, Ciˆencia e Tecnologia do Estado de Mato Grosso do Sul (Fundect); Museu das Culturas Dom Bosco. Conference Chair Nalvo Franco de Almeida Jr. Universidade Federal de Mato Grosso do Sul, Brazil Program Chairs Marcilio C.P. de Souto Universidade Federal de Pernambuco, Brazil Maricel G. Kann UniversityofMarylandBaltimoreCounty,USA Steering Comittee Marcelo de Macedo Br´ıgido Universidade de Bras´ılia,Brazil Ivan Gesteira Costa Universidade Federal de Pernambuco, Brazil Osmar Norberto de Sousa Pontif´ıcia Universidade Cat´olica do Rio Grande do Sul, Brazil Carlos Eduardo Ferreira Universidade de Sa˜o Paulo, Brazil Joa˜o Carlos Setubal Universidade de Sa˜o Paulo, Brazil Guilherme P. Telles Universidade Estadual de Campinas, Brazil Maria Emilia Walter Universidade de Bras´ılia,Brazil Program Committee Said S. Adi Universidade Federal de Mato Grosso do Sul, Brazil Nalvo F. Almeida Jr. Universidade Federal de Mato Grosso do Sul, Brazil Fernando A´lvarez-Val´ın Universidad de la Republica, Uruguay Ana L.C. Bazzan Universidade Federal do Rio Grande do Sul, Brazil Ana M. Benko-Iseppon Universidade Federal de Pernambuco, Brazil Mar´ılia D.V. Braga INMETRO, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia,Brazil VIII Organization Yana Bromberg Rutgers University, USA Emidio Capriotti University of the Balearic Islands, Spain Alessandra Carbone Pierre and Marie Curie University, France Ivan Gesteira Costa Universidade Federal de Pernambuco, Brazil Mark Craven University of Wisconsin, USA Alberto Da´vila Fiocruz, Brazil Andr´e C.P.L.F. de Carvalho Universidade de Sa˜o Paulo/Sa˜o Carlos, Brazil Osmar Norberto de Souza Pontif´ıciaUniversidadeCat´olicadoRioGrande do Sul, Brazil Zanoni Dias Universidade Estadual de Campinas, Brazil Carlos E. Ferreira Universidade de Sa˜o Paulo, Brazil Andr´e Fujita Universidade de Sa˜o Paulo, Brazil Katia S. Guimara˜es Universidade Federal de Pernambuco, Brazil Ronaldo F. Hashimoto Universidade de Sa˜o Paulo, Brazil Dirk Husmeier University of Glasgow, UK Ney Lemke Universidade Estadual Paulista Ju´lio de Mesquita Filho, Brazil Sergio Lifschitz Pontif´ıcia Universidade Cat´olica do Rio de Janeiro, Brazil Ana Carolina Lorena Universidade Federal do ABC, Brazil Thomas Madej NIH, USA Ion Mandoiu University of Connecticut, USA Natalia F. Martins Embrapa, Brazil Marta Mattoso Universidade Federal do Rio de Janeiro, Brazil Satoru Miyano University of Tokyo, Japan Jose Carlos M. Mombach Universidade Federal de Santa Maria, Brazil Ivan Ovcharenko NIH, USA Mathew Palakal Indiana University/Purdue University Indianapolis, USA Anna Panchenko NIH, USA Sergio Pantano Instituto Pasteur de Montevideo, Uruguay Gustavo Parisi Universidad Nacional de Quilmes, Argentina Fa´bio de Oliveira Pedrosa Universidade Federal do Parana´,Brazil Natasa Przulj Imperial College, UK Duncan Ruiz Pontif´ıciaUniversidadeCat´olicadoRioGrande do Sul, Brazil Marie-France Sagot INRIA, France Cenk Sahinalp Simon Fraser University, Canada Alexander Schliep Rutgers University, USA Joa˜o Setubal Universidade de Sa˜o Paulo, Brazil Roded Sharan Tel Aviv University, Israel Hagit Shatkay University of Delaware, USA Peter F. Stadler University of Leipzig, Germany Guilherme P. Telles Universidade Estadual de Campinas, Brazil Claudio Valverde Universidad Nacional de Quilmes, Argentina Maria Emilia T. Walter Universidade de Bras´ılia,Brazil Organization IX Additional Reviewers Paulo Alvarez Universidade de Bras´ılia,Brazil Ronnie Alves Universidade Federal do Rio Grande do Sul, Brazil George Cavalcanti Universidade Federal de Pernambuco, Brazil Guillaume Cleuziou Universit´e d’Orl´eans,France Andr´e Coelho Universidade de Fortaleza, Brazil Bruno Motta de Carvalho Universidade Federal do Rio Grande do Norte, Brazil Marcelo Henriques de Carvalho Universidade Federal de Mato Grosso do Sul, Brazil Daniel de Oliveira Universidade Federal do Rio de Janeiro, Brazil Katti Faceli Universidade Federal de S˜ao Carlos/Sorocaba, Brazil Cristina Fernandes Universidade de Sa˜o Paulo, Brazil Celina Figueiredo Universidade Federal do Rio de Janeiro, Brazil Alvaro Franco Universidade de Sa˜o Paulo, Brazil Alexandre Freire Universidade de Sa˜o Paulo, Brazil Chih-Hao Hsu NIH, USA Andre Kashiwabara Universidade Tecnolo´gica Federal do Paran´a, Brazil Marta Kwiatkowska University of Oxford, UK Ivani Lopes Embrapa, Brazil Fa´bio Martinez Universidade Federal de Mato Grosso do Sul, Brazil Karina S. Machado Universidade Federal do Rio Grande, Brazil Leandro Marzulo Universidade do Estado do Rio de Janeiro, Brazil Mariana Mendoza Universidade Federal do Rio Grande do Sul, Brazil Luciana Montera Universidade Federal de Mato Grosso do Sul, Brazil Deborah Muganda University of Wisconsin, USA Alexandre Noma Universidade Federal do ABC, Brazil Kary Ocan˜a Universidade Federal do Rio de Janeiro, Brazil Thiago Lipinski Paes Pontif´ıciaUniversidadeCat´olicadoRioGrande do Sul, Brazil Ronaldo Prati Universidade Federal do ABC, Brazil Paula Andreia Silva Universidade Cato´lica de Bras´ılia,Brazil Renata Souza Universidade Federal de Pernambuco, Brazil Jens Stoye Universita¨t Bielefeld, Germany Renato Tin´os Universidade de Sa˜o Paulo/Ribeira˜o Preto, Brazil Adriano Werhli Universidade Federal do Rio Grande, Brazil Cleber Zanchettin Universidade Federal de Pernambuco, Brazil X Organization Financial Sponsors Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnol´ogico (CNPq) Coordenac¸˜ao de Aperfeic¸oamento de Pessoalde N´ıvel Superior (CAPES) Fundac¸˜ao de Apoio ao Desenvolvimento do Ensino, Ciˆencia e Tecnologia do Estado de Mato Grosso do Sul (Fundect) Fundac¸˜ao de Apoio a` Pesquisa ao Ensino e a` Cultura (FAPEC) Unidade Especial de Criac¸˜ao e Inova¸c˜ao da Prefeitura Municipal de Campo Grande Governo do Estado de Mato Grosso do Sul Life Technologies Copagaz H2L Soluc¸˜oes para Documentos Netware Enterprise Alfa Computadores Tecsinapse Paulist˜ao Infor-7 Table of Contents Transposition Diameter and Lonely Permutations .................... 1 Lu´ıs Felipe I. Cunha, Luis Antonio B. Kowada, Rodrigo de A. Hausen, and Celina M.H. de Figueiredo Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes.................................... 13 Pedro Feijao and Joao Meidanis On the Approximation Ratio of Algorithms for Sorting by Transpositions without Using Cycle Graphs ...................... 25 Gustavo Rodrigues Galva˜o and Zanoni Dias A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats...................................... 37 A.A. Matroud, C.P. Tuffley, D. Bryant, and M.D. Hendy RNA Folding Algorithms with G-Quadruplexes ...................... 49 Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Ho¨ner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, and Peter F. Stadler Molecular Dynamics for Simulating the Protein Folding Process Using the 3D AB Off-Lattice Model...................................... 61 C´esar Manuel Vargas Ben´ıtez and Heitor Silv´erio Lopes A Bioconductor Based Workflow for Z-DNA Region Detection and Biological Inference........................................... 73 Halian Vilela, Taina´ Raiol, Andrea Queiroz Maranha˜o, Maria Em´ılia Walter, and Marcelo M. Br´ıgido A Probabilistic Model Checking Approach to Investigate the Palytoxin Effects on the Na+/K+-ATPase.................................... 84 Fernando A.F. Braz, Jader S. Cruz, Alessandra C. Faria-Campos, and S´ergio V.A. Campos RFMirTarget: A Random Forest Classifier for Human miRNA Target Gene Prediction ................................................. 97 Mariana R. Mendoza, Guilherme C. da Fonseca, Guilherme L. de Morais, Ronnie Alves, Ana L.C. Bazzan, and Rogerio Margis
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