Bioinformatics Tools and Applications
Biology has progressed tremendously in the last decade due in part to the increased automation in the generation of data from sequences to genotypes to phenotypes. Biology is now very much an information science and bioinformatics provides the means to co
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David Edwards Jason Stajich David Hansen ●
Editors
Bioinformatics Tools and Applications
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Editors David Edwards Australian Centre for Plant Functional Genomics Institute for Molecular Biosciences and School of Land Crop and Food Sciences University of Queensland Brisbane, QLD 4072 Australia
David Hansen Australian E-Health Research Centre CSIRO Qld 4027, Brisbane, Australia
Jason Stajich Department of Plant Pathology and Microbiology University of California Berkeley, CA USA
ISBN 978-0-387-92737-4 e-ISBN 978-0-387-92738-1 DOI 10.1007/978-0-387-92738-1 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2009927717 © Springer Science+Business Media, LLC 2009 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
Preface
Biology has progressed tremendously in the last decade due in part to the increased automation in the generation of data from sequences to genotypes to phenotypes. Biology is now very much an information science, and bioinformatics provides the means to connect biological data to hypotheses. Within this volume, we have collated chapters describing various areas of applied bioinformatics, from the analysis of sequence, literature, and functional data to the function and evolution of organisms. The ability to process and interpret large volumes of data is essential with the application of new high throughput DNA sequencers providing an overload of sequence data. Initial chapters provide an introduction to the analysis of DNA and protein sequences, from motif detection to gene prediction and annotation, with specific chapters on DNA and protein databases as well as data visualization. Additional chapters focus on gene expression analysis from the perspective of traditional microarrays and more recent sequence-based approaches, followed by an introduction to the evolving field of phenomics, with specific chapters detailing advances in plant and microbial phenome analysis and a chapter dealing with the important issue of standards for functional genomics. Further chapters present the area of literature databases and associated mining tools which are becoming increasingly essential to interpret the vast volume of published biological information, while the final chapters present bioinformatics pure
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