by Jean-Michel Claverie,PhD and Cedric Notredame,PhD Bioinformatics FOR DUMmIES ‰ 2ND EDITION 01_089857 ffirs.qxp 11/6/06 3:39 PM Page iii 01_089857 ffirs.qxp 11/6/06 3:39 PM Page ii Bioinformatics FOR DUMmIES ‰ 2ND EDITION 01_089857 ffirs.qxp 11/6/06 3:39 PM Page i 01_089857 ffirs.qxp 11/6/06 3:39 PM Page ii by Jean-Michel Claverie,PhD and Cedric Notredame,PhD Bioinformatics FOR DUMmIES ‰ 2ND EDITION 01_089857 ffirs.qxp 11/6/06 3:39 PM Page iii Bioinformatics For Dummies®, 2nd Edition Published by Wiley Publishing, Inc. 111 River Street Hoboken, NJ 07030-5774 www.wiley.com Copyright © 2007 by Wiley Publishing, Inc., Indianapolis, Indiana Published by Wiley Publishing, Inc., Indianapolis, Indiana Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as permit- ted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600. 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Library of Congress Control Number: 2006934844 ISBN13: 978-0-470-08985-9 ISBN10: 0-470-08985-7 Manufactured in the United States of America 10 9 8 7 6 5 4 3 2 1 1B/SX/RR/QW/IN 01_089857 ffirs.qxp 11/6/06 3:39 PM Page iv About the Authors Jean-Michel Claverie is Professor of Medical Bioinformatics at the School of Medicine of the Université de la Méditerranée, and a consultant in genomics and bioinformatics. He is the founder and current head of the Structural & Genomic Information Laboratory, located in Marseilles, a sunny city on the Mediterranean coast of France. Using science as a pretext to travel, Jean-Michel has held positions in Paris (France), Sherbrooke (PQ, Canada), the Salk Institute (La Jolla, CA), the Pasteur Institute (Paris), Incyte pharma- ceutical (Palo Alto, CA); and the National Center for Biotechnology Information (Bethesda, MD). He has used computers in biology since the early days –– his Ph.D. work involved modeling biochemi- cal reactions by programming an 8K Honeywell 516 computer right from the console switches! Although he has no clear recollection of it, he has been credited with introducing the French word “bioinfor- matique” in the late eighties, before involuntarily coining the catchy “bioinformatics” by mistranslating it while giving a talk in English! Jean-Michel’s current research interests are in microbial and struc- tural genomics, and in the development of bioinformatic methods for the prediction of gene function. He is the author or coauthor of more than 150 scientific publications, and a member of numerous international review panels and scientific councils. In his spare time, he enjoys the relaxed pace of life in Marseilles, with his wife Chantal and their two sons, Nicholas and Raphael. Cedric Notredame is a researcher at the French National Centre for Scientific Research. Cedric has used and abused the facilities offered by science to wander around Europe. After a Ph.D. at EMBL (Heidelberg, Germany) and at the European Bioinformatics Institute (Cambridge, UK) under the supervision of Des Higgins (yes, the ClustalW guy), Cedric did a post-doc at the National Institute of Medical Research (London, UK), in the lab of Willie Taylor and under the supervision of Jaap Heringa. He then did a post-doc in Lausanne (Switzerland) with Phillip Bucher, and remained involved with the Swiss Institute of Bioinformatics for several years. Having had his share of rain, snow, and wind, Cedric has finally settled in Marseilles, where the sun and the sea are simply warmer than any other place he has lived in. Cedric dedicates most of his research to the multiple sequence alignment problem and its many applications in biology. His friends claim that his entire life (past, present, future) is somehow stuffed into the T-Coffee multiple-sequence alignment package. When he is not busy dismantling T-Coffee and brewing new sequences, Cedric enjoys life in the company of his wife, Marita. 01_089857 ffirs.qxp 11/6/06 3:39 PM Page v 01_089857 ffirs.qxp 11/6/06 3:39 PM Page vi Dedication This is for my parents Monique and Jack, for keeping me in school, and for Chantal, for keeping me happy — in and out of the lab. It’s also for my daugh- ter Vanessa, and my sons Nicholas and Raphael, for reminding me that not everything in life is scientific. –– J-MC This is for my wife Marita, my daughter Lina, my mother Marie and in memory of my grandparents, Simone and Louis. –– CN Authors’ Acknowledgments The entire Wiley staff did a great job pulling together to publish this book on tight deadlines. We’d especially like to thank our tireless project editor, Paul Levesque, and Barry Childs-Helton, who did a great job copyediting a text full of obscure biochemical words. We’d also like to thank Amey Godse, our technical editor. Amey nailed down major and minor inaccuracies alike. His many suggestions did much to improve the book. We also have to thank the bioinformatics community for creating the many great Web resources that we describe in this book and for making them avail- able for free over the Internet. We personally know a number of the folks who keep these sites up and running –– and salute all of them for their hard work, enthusiasm, and dedication. Topping this list are the staff members of the Swiss Bioinformatics Institute, who run the ExPASy and the Swiss EMBnet Web server. They always went out of their way to answer any query regarding their site. The NCBI folks have also been very helpful, and we thank them for that. We also want to pat each other on the back for making the writing of this book great fun! Finally, we’d like to thank our families and friends, who put up with missed dinners, extra child care, changing deadlines, late nights, and the many other demands of a project like this. We really appreciate their patience –– and promise that we won’t do another one . . . at least not anytime soon! 01_089857 ffirs.qxp 11/6/06 3:39 PM Page vii