Table Of Content

Bioinformatics: Concepts, Methodologies, Tools, and Applications Information Resources Management Association USA Managing Director: Lindsay Johnston Editorial Director: Joel Gamon Assistant Acquisitions Editor: Kayla Wolfe Book Production Manager: Jennifer Yoder Publishing Systems Analyst: Adrienne Freeland Development Editor: Chris Wozniak Assistnt Book Production Editor: Deanna Jo Zombro Cover Design: Jason Mull Published in the United States of America by Medical Information Science Reference (an imprint of IGI Global) 701 E. Chocolate Avenue Hershey PA 17033 Tel: 717-533-8845 Fax: 717-533-8661 E-mail: [email protected] Web site: http://www.igi-global.com Copyright © 2013 by IGI Global. All rights reserved. No part of this publication may be reproduced, stored or distributed in any form or by any means, electronic or mechanical, including photocopying, without written permission from the publisher. Product or company names used in this set are for identification purposes only. Inclusion of the names of the products or companies does not indicate a claim of ownership by IGI Global of the trademark or registered trademark. Library of Congress Cataloging-in-Publication Data Bioinformatics : concepts, methodologies, tools, and applications / Information Resources Management Association, editors. volumes cm Includes bibliographical references and index. ISBN 978-1-4666-3604-0 (hardcover) -- ISBN 978-1-4666-3606-4 (print & perpetual access) -- ISBN 978-1-4666-3605-7 (ebook) 1. Bioinformatics. I. Information Resources Management Association. QH324.2.B54734 2013 572.80285--dc23 2012049182 British Cataloguing in Publication Data A Cataloguing in Publication record for this book is available from the British Library. The views expressed in this book are those of the authors, but not necessarily of the publisher. Editor-in-Chief Mehdi Khosrow-Pour, DBA Contemporary Research in Information Science and Technology, Book Series Associate Editors Steve Clarke, University of Hull, UK Murray E. Jennex, San Diego State University, USA Annie Becker, Florida Institute of Technology, USA Ari-Veikko Anttiroiko, University of Tampere, Finland Editorial Advisory Board Sherif Kamel, American University in Cairo, Egypt In Lee, Western Illinois University, USA Jerzy Kisielnicki, Warsaw University, Poland Keng Siau, University of Nebraska-Lincoln, USA Amar Gupta, Arizona University, USA Craig van Slyke, University of Central Florida, USA John Wang, Montclair State University, USA Vishanth Weerakkody, Brunel University, UK List of Contributors Abdullah, Azween / University Technology PATRONAS, Malaysia ................................................1745 Adamaki, Maria / University of Athens, Greece .............................................................................1025 Ahmad, Muneer / King Faisal University, Saudi Arabia ................................................................1745 Ahsan, Syed / University of Engineering and Technology, Pakistan .................................................345 Aidinis, Vasilis / Biomedical Sciences Research Center “Alexander Fleming,” Greece ................1196 Ali, Hesham / University of Nebraska at Omaha, USA & University of Nebraska Medical Center, USA .................................................................................................................................1536 Al-Naymat, Ghazi / University of Tabuk, Saudi Arabia ....................................................................222 Alvarez, Marco A. / Utah State University, United States ..................................................................93 Alves de Melo, Alba Cristina Magalhaes / University of Brasilia, Brazil .......................................605 Anand, Swadha / National Institute of Immunology, India .............................................................1642 Ane, Bernadetta Kwintiana / Universität Stuttgart, Germany .......................................................1570 Angelopoulos, Nicos / Edinburgh University, UK .............................................................................364 Apparao, Allam / Jawaharlal Nehru Technological University, India .............................................948 Appel, Ana Paula / Federal University of Espirito Santo at São Mateus, Brazil .............................446 Arai, Hiroyuki / Tohoku University, Japan .......................................................................................438 Archer, John A. C. / King Abdullah University of Science and Technology, Kingdom of Saudi Arabia ...............................................................................................................................1522 Asraf, S. Sheik / Madurai Kamaraj University, India .....................................................................1354 Azar, Ahmad Taher / Modern Science and Arts University, Egypt .......................................................1 Bae, Seung-Hee / Indiana University - Bloomington, USA ...............................................................287 Bajic, Vladimir B. / King Abdullah University of Science and Technology, Kingdom of Saudi Arabia ...............................................................................................................................1522 Bapi, Raju S. / University of Hyderabad, India. ................................................................................937 Batmaz, Inci / Middle East Technical University, Turkey ...................................................................42 Beason, Scott / Computer Sciences Corporation, USA......................................................................287 Beever, Jonathan / Purdue University, USA ....................................................................................1405 Beligiannis, Grigorios / University of Western Greece, Greece ........................................................805 Benos, Panayiotis V. / University of Pittsburgh, USA .......................................................................513 Bernstein, Richard / Cornell University, USA ..................................................................................273 Bertucci, François / Inserm, Paoli Calmettes Institute, France ........................................................151 Bhardwaj, Minakshi / Cardiff University, UK ................................................................................1334 Bhattacharya, Arnab / Indian Institute of Technology Kanpur, India ............................................1599 Bhavani, S.Durga / University of Hyderabad, India. ........................................................................937 Bidaut, Ghislain / Inserm, Paoli Calmettes Institute, France ...........................................................151 Birnbaum, Daniel / Inserm, Paoli Calmettes Institute, France ........................................................151 Borboudakis, G. / ICS-FORTH, Greece & University of Crete, Greece ...........................................586 Buabin, Emmanuel / Methodist University College Ghana, Ghana ................................................761 Cai, Meihong / Nanjing University, China ......................................................................................1184 Cárdenas, Martha-Ivón / Universitat Politècnica de Catalunya, Spain ..........................................817 Chatziioannou, Aristotle / National Hellenic Research Foundation, Greece ................................1283 Chen, Jake Y. / Indiana Center for Systems Biology and Personalized Medicine, USA; Indiana University, USA & Purdue University, USA ...............................................................................1378 Chen, Xin / Zhejiang University, China ...........................................................................................1174 Chen, Zheng / Beijing Geriatric Hospital, China .............................................................................268 Choi, Jong Youl / Indiana University - Bloomington, USA ...............................................................287 Chowdhary, Rajesh / Biomedical Informatics Research Center, USA ............................................1522 Christodoulou, E. G. / BIOTEC Technische Universität Dresden, Germany ...................................586 Chui, Dehua / Peking University, China & Third Hospital of Peking University, China .................268 Corbit, Margaret / Cornell University, USA .....................................................................................273 Cui, Jun / Nanjing University, China ...............................................................................................1184 Culbertson, Adam / Indiana University, USA .................................................................................1378 Currall, Benjamin / Creighton University, USA .............................................................................1536 Dang, Loan Thi-Tung / Vietnam National University, Vietnam ........................................................920 Daniel, Varghese M / Monash University, Australia .........................................................................249 Degenkolbe, Elisa / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Germany ..............................................................................................1252 Dempsey, Kathryn / University of Nebraska at Omaha, USA & University of Nebraska Medical Center, USA .................................................................................................................................1536 Deng, Si / South China University of Technology, China ...................................................................798 Deris, Safaai / Universiti Teknologi Malaysia, Malaysia ................................................................1727 deVersterre, Lori Watrous / New Jersey Institute of Technology, USA .........................................1306 Dileep, A. D. / Indian Institute of Technology Madras, India ..............................................................72 Dimitrakopoulos, Christos M. / University of Patras, Greece ......................................................1237 Ding, Wei / Merck & Co., Inc., USA ..................................................................................................465 Döring, Ole / HGI-Charité Berlin, Germany ...................................................................................1344 Doukas, Charalampos / University of the Aegean, Greece ............................................................1283 Dunham, Margaret H. / Southern Methodist University, USA .......................................................1705 Dutta, Sourav / IBM Research Lab, India .......................................................................................1599 Ekanayake, Jaliya / Indiana University - Bloomington, USA ...........................................................287 Ekanayake, Saliya / Indiana University - Bloomington, USA ..........................................................287 Emili, Andrew / University of Toronto, Canada ................................................................................831 Facelli, Julio Cesar / The University of Utah, USA ...........................................................................195 Faloutsos, Christos / Carnegie Mellon University, USA ...................................................................446 Famili, Fazel / National Research Council, Canada .........................................................................513 Fan, Dongsheng / Third Hospital of Peking University, China .........................................................268 Feng, Wenqing / Accela Sciences, LLC, USA ....................................................................................465 Finetti, Pascal / Inserm, Paoli Calmettes Institute, France ...............................................................151 Fliss, Ismail / Université Laval, Canada..........................................................................................1755 Fox, Geoffrey / Indiana University - Bloomington, USA ...................................................................287 Fukuyama, Hidenao / Kyoto University Graduate School of Medicine, Japan ...............................427 Furukawa, Katsutoshi / Tohoku University, Japan ..........................................................................438 Furumoto, Shozo / Tohoku University, Japan ...................................................................................438 Gao, Xieping / Xiangtan University, China .......................................................................................786 Garcia-Manteiga, Jose M. / Protein Transport and Secretion Unit, San Raffaele – DIBIT, Italy .............................................................................................................................................1494 Garcia, Maxime / Inserm, Paoli Calmettes Institute, France ...........................................................151 Gardiner, Eleanor Joyce / University of Shefield, UK ...................................................................1126 Georgopoulos, Efstratios F. / Technological Educational Institute of Kalamata, Greece .............1237 Ghiggi, Athos / University of Lugano, Switzerland ...........................................................................884 Giraldo, Jesús / Universitat Autònoma de Barcelona, Spain ............................................................817 Gondro, Cedric / The Centre for Genetic Analysis and Applications, University of New England, Australia ........................................................................................................................................105 Grover, Abhinav / Indian Institute of Technology, India ...................................................................330 Gunarathne, Thilina / Indiana University - Bloomington, USA .......................................................287 Gunasekaran, P. / Madurai Kamaraj University, India ..................................................................1354 Hadjiprocopis, Andreas / Higher Technical Institute, Cyprus .........................................................364 Hallworth, Richard / Creighton University, USA ...........................................................................1536 Hammami, Riadh / Université Laval, Canada ...............................................................................1755 Hattori, Masahiro / Tokyo University of Technology, Japan ............................................................986 Herwig, Ralf / Max Planck Institute for Molecular Genetics, Germany .........................................1072 Hu, Pingzhao / York University, Canada & University of Toronto, Canada .....................................831 Hurdle, John F. / The University of Utah, USA .................................................................................195 Hussain, Pz Tasaduq / University of Kashmir, India ......................................................................1424 Iqbal, Mir Javid / University of Kashmir, India ..............................................................................1424 Ishaq, Geer Mohammad / University of Kashmir, India ................................................................1424 Jankovic, Boris R. / King Abdullah University of Science and Technology, Kingdom of Saudi Arabia ...............................................................................................................................1522 Jiang, Hui / York University, Canada ................................................................................................831 Jose, Jimmy / University of Nizwa, Oman .......................................................................................1453 Junior, Caetano Traina / University of São Paulo at São Carlos, Brazil .........................................446 Jyothi, Koona Saradha / Andhra University, India ..........................................................................948 Kafetzopoulos, Dimitris / ICS-Forth, Greece .................................................................................1676 Kaforou, Soia / IMBB-Forth, Greece .............................................................................................1676 Kalia, Awdhesh / University of Louisville, USA ................................................................................745 Kalina, Jan / Institute of Computer Science of the Academy of Sciences of the Czech Republic, Czech Republic ............................................................................................................................1113 Kandpal, K. N. / Indian Veterinary Research Institute, India .........................................................1564 Kane, Michael D. / Purdue University, USA ...................................................................................1405 Khan, Mohammad Faheem / Indian Veterinary Research Institute, India ....................................1564 Khoon, Chan Chee / Universiti Sains Malaysia, Malaysia ..............................................................240 Koksal, Guser / Middle East Technical University, Turkey .................................................................42 Kossida, Sophia / Biomedical Research Foundation of the Academy of Athens, Greece ..................805 Kotamarti, Rao M. / Southern Methodist University, USA .............................................................1705 Kotera, Masaaki / Kyoto University, Japan ......................................................................................986 Koultouki, Eleftheria / University of Athens, Greece .....................................................................1025 Krishnaveni, Marimuthu / Avinashilingam Deemed University for Women, Thadagam Post, India ............................................................................................................................................1570 Küçükural, Alper / University of Kansas, USA & Sabanci University, Turkey ................................386 Kudo, Yukitsuka / Tohoku University, Japan ....................................................................................438 Kumar, Sonu / Indian Institute of Technology, India ........................................................................330 Kwan, Paul / University of New England, Australia .........................................................................105 Lambrou, George I. / University of Athens, Greece .......................................................................1025 Lian, Yongsheng / University of Louisville, USA ..............................................................................745 Liberati, Diego / Italian National Research Council, Italy, Italian National Nuclear Physics Institute, Italy & Politecnico di Milano University, Italy .............................................................664 Li, Bin / Merrimack Pharmaceuticals, USA ......................................................................................690 Lidbury, Brett A. / Australian National University, Australia ..................................................29, 1474 Likothanassis, Spiridon D. / University of Patras, Greece ....................................................805, 1237 Li, Miaoxin / Shanghai Center for Bioinformation Technology, China ............................................570 Liu, Jing / China Agricultural University, China ............................................................................1667 Liu, Jun-Qian / Kagawa University, Japan .......................................................................................432 Liu, Tingting / Peking University, China ...........................................................................................268 Liu, Wei / Agios Pharmaceuticals Inc, USA ......................................................................................173 Liu, Xinying / Peking University, China............................................................................................268 Liu, Yan-Hui / Merck & Co., Inc., USA .............................................................................................465 Lu, Jiangyang / First Afiliated Hospital of General Hospital of PLA, China ..................................268 Luo, Lixin / South China University of Technology, China ...............................................................798 Maglogiannis, Ilias / University of Central Greece, Greece ...........................................................1283 Martín-Merino, Manuel / University Pontiicia of Salamanca, Spain ...........................................1609 Martin, Victoria / George Mason University, USA ...........................................................................130 Masso, Majid / George Mason University, USA ..............................................................................1010 Matsumoto, Yoshiki / Kagawa University, Japan .............................................................................432 Maulik, Ujjwal / Jadavpur University, India ..................................................................................1626 Mavroudi, Seferina P. / University of Patras, Greece ....................................................................1237 Meslin, Eric M. / Indiana University Center for Bioethics, USA & Indiana University, USA ........1378 Miki, Takanori / Kagawa University, Japan .....................................................................................432 Mitchell, Joyce A. / The University of Utah, USA .............................................................................195 Mohanty, Debasisa / National Institute of Immunology, India........................................................1642 Montemanni, Roberto / Istituto Dalle Molle di Studi sull’Intelligenza Artiiciale, Switzerland ......884 Moore, Jason H. / Dartmouth Medical School, USA ........................................................................725 Morar, Nicolae / Purdue University, USA .......................................................................................1405 Moreano, Nahri / Federal University of Mato Grosso do Sul, Brazil ...............................................605 Mori, Hiroshi / Osaka City University Medical School, Japan .......................................................1557 Moschopoulos, Charalampos / Biomedical Research Foundation of the Academy of Athens, Greece & University of Patras, Greece ........................................................................................805 Moschovi, Maria / University of Athens, Greece ............................................................................1025 Murray, Stuart / Agios Pharmaceuticals Inc, USA ...........................................................................173 Mushtaq, Mohsin Bin / Sindh Medical College, Pakistan & Dow University of Health Sciences, Pakistan .......................................................................................................................................1424 Natarajan, Madhusudan / Pizer, USA .............................................................................................552 Nikolaidou-Katsaridou, Maria Nefeli / Biomedical Sciences Research Center “Alexander Fleming,” Greece ........................................................................................................................1196 Nikolova, Elena V. / Bulgarian Academy of Sciences, Bulgaria .....................................................1072 Nikolov, S. / Institute of Mechanics and Biomechanics, Bulgaria .....................................................851 Nikolov, Svetoslav G. / Bulgarian Academy of Sciences, Bulgaria ................................................1072 Norton-Barker, Catherine / Cornell University,USA .......................................................................273 Nyeki, Catherine / Plurimedia Artist,“plasticienne”, France ........................................................1441 Okamura, Nobuyuki / Tohoku University, Japan .............................................................................438 Olier, Iván / The University of Manchester, UK ................................................................................817 Palshikar, Girish Keshav / Tata Research Development and Design Centre, India ........................400 Pan, Youlian / National Research Council, Canada ..........................................................................513 Paparountas, Triantafyllos / Biomedical Sciences Research Center “Alexander Fleming,” Greece .........................................................................................................................................1196 Pattin, Kristine A. / Dartmouth Medical School, USA......................................................................725 Penchovsky, Robert / Soia University “St. Kliment Ohridski”, Bulgaria .......................................860 Petrov, Valko G. / Bulgarian Academy of Sciences, Bulgaria .........................................................1072 Phan, Ngoc Kim / Vietnam National University, Vietnam .................................................................920 Popescu, George V. / University Politehnica Bucharest, Romania ...................................................676 Popescu, Sorina C. / Boyce Thompson Institute for Plant Research, USA .......................................676 Potamias, George / ICS-Forth, Greece ...........................................................................................1676 Prasanthi, S. / University of Hyderabad, India. ................................................................................937 Punetha, Ankita / Indian Institute of Technology, India ...................................................................330 Putty, Kalyani / University of Louisville, USA ..................................................................................745 Qiu, Judy / Indiana University - Bloomington, USA .........................................................................287 Qiu, Ping / Merck & Co., Inc., USA ...................................................................................................465 Qi, Xiaojun / Utah State University, United States ..............................................................................93 Rajnish, K.N. / Madurai Kamaraj University, India .......................................................................1354 Rani, T. Sobha / University of Hyderabad, India. .............................................................................937 Rao, B. Subba / Andhra University, India .........................................................................................948 Rawat, S. S. / Indian Veterinary Research Institute, India ..............................................................1564 Reddy, Padmalatha S. / Pizer, USA .................................................................................................173 Remli, Muhammad Akmal / Universiti Teknologi Malaysia, Malaysia ........................................1727 Reyes, Vicente M. / Rochester Institute of Technology, Rochester, USA .........................................1158 Rho, Mina / Indiana University - Bloomington, USA ........................................................................287 Røe, O. D. / Levanger Hospital—Nord-Trøndelag Health Trust, Norway, & Norwegian University of Science and Technology, Norway ............................................................................586 Roller, Dieter / Universität Stuttgart, Germany ...............................................................................1570 Rovira, Xavier / Universitat Autònoma de Barcelona, Spain ...........................................................817 Ruan, Yang / Indiana University - Bloomington, USA ......................................................................287 Rustici, Gabriella / European Molecular Biology Laboratory-European Bioinformatics Institute, UK ................................................................................................................................1196 Sakr, Sherif / University of New South Wales, Australia ...................................................................222 Sarkar, Anasua / Government College of Engineering and Leather Technology, India .................1626 Sarkar, Anita / Indian Institute of Technology, India ........................................................................330 Satoh, Jun-Ichi / Meiji Pharmaceutical University, Japan ...............................................................964 Schaefer, Ulf / King Abdullah University of Science and Technology, Kingdom of Saudi Arabia .........................................................................................................................................1522 Seemann, Petra / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Germany ..............................................................................................1252 Sekhar, C. Chandra / Indian Institute of Technology Madras, India .................................................72 Serenko, Natalia / Lakehead University, Canada ...........................................................................1317 Sethu, Palaniappan / University of Louisville, USA .........................................................................745 Sezerman, O. Uğur / Sabanci University, Turkey .............................................................................386 Shah, Abad / University of Engineering and Technology, Pakistan ..................................................345 Shen, Pingping / Nanjing University, China....................................................................................1184 Shen, Yong / Center for Advanced Therapeutic Strategies for Brain Disorders, Raskamp Institute, USA ................................................................................................................................322 Sheth, Vrunda / Rochester Institute of Technology, Rochester, USA ...............................................1158 Shi, Pan / The Pennsylvania State University, USA .........................................................................1378 Shi, Zhiao / Vanderbilt University, USA ............................................................................................637 Shyr, Yu / Vanderbilt University, USA Yixue Li Shanghai Center for Bioinformation Technology, China .............................................................................................................................................570 Singh, Amardeep / Punjabi University, India .................................................................................1769 Singh, Shailendra / PEC University of Technology, India ..............................................................1769 Singhera, Zafar / Oracle Corporation, USA .....................................................................................345 Song, Min / New Jersey Institute of Technology, USA .....................................................................1306 Sotoca, Ana M. / Radboud University, The Netherlands .................................................................1688 Sprague, Jon E. / Ohio Northern University, USA ..........................................................................1405 Springer, John A. / Purdue University, USA ...................................................................................1405 Sridhar, G. R. / Endocrine and Diabetes Centre, India ....................................................................948 Srinivas, Kudipudi / V R Siddhartha Engineering College, India ....................................................948 Stahl, Olivier / Inserm, Paoli Calmettes Institute, France ................................................................151 Subhasini, Parthasarathy / Avinashilingam Deemed University for Women, Thadagam Post, India ............................................................................................................................................1570 Sundar, Durai / Indian Institute of Technology, India .......................................................................330 Sun, Miao / Peking University, China ................................................................................................268 Sun, Tingzhe / Nanjing University, China .......................................................................................1184 Szilagyi, Andras / University of Kansas, USA ...................................................................................386 Takeuchi, Yoshiki / Kagawa University, Japan .................................................................................432 Tang, Haixu / Indiana University - Bloomington, USA .....................................................................287 Tao, Yi-Min / China Agricultural University, China .......................................................................1667 Tashiro, Manabu / Tohoku University, Japan ...................................................................................438 Tchagang, Alain B. / National Research Council, Canada ...............................................................513 Tewik, Ahmed H. / University of Minnesota, USA ...........................................................................513 Theoilatos, Konstantinos A. / University of Patras, Greece .........................................................1237

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As a result of experimental techniques, the combination of biology and computer science was initiated to classify and process an expanding number of biological observations.Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the

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