Praise for the third edition of Bioinformatics
‘This book is a gem to read and use in practice.’
–Briefings in Bioinformatics
‘This volume has a distinctive, special value as it offers an unrivalled level of details and unique expert insights from the leading computational biologists, including the very creators of popular bioinformatics tools.’
–Chem Bio Chem
‘A valuable survey of this fascinating field. . . I found it to be the most useful book on bioinformatics that I have seen and recommend it very highly.’
–American Society for Microbiology News
‘This should be on the bookshelf of every molecular biologist.’
–The Quarterly Review of Biolog’
The field of bioinformatics is advancing at a remarkable rate. With the development of new analytical techniques that make use of the latest advances in machine learning and data science, today’s biologists are gaining fantastic new insights into the natural world’s most complex systems. These rapidly progressing innovations can, however, be difficult to keep pace with.
The expanded fourth edition of the best-selling Bioinformatics aims to remedy this by providing students and professionals alike with a comprehensive survey of the current field. Revised to reflect recent advances in computational biology, it offers practical instruction on the gathering, analysis, and interpretation of data, as well as explanations of the most powerful algorithms presently used for biological discovery. Bioinformatics, Fourth Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists at all levels, covering both key concepts that have stood the test of time and the new and important developments driving this fast-moving discipline forwards.
This new edition features:
* New chapters on metabolomics, population genetics, metagenomics and microbial community analysis, and translational bioinformatics
* A thorough treatment of statistical methods as applied to biological data
* Special topic boxes and appendices highlighting experimental strategies and advanced concepts
* Annotated reference lists, comprehensive lists of relevant web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics
Bioinformatics is an indispensable companion for researchers, instructors, and students of all levels in molecular biology and computational biology, as well as investigators involved in genomics, clinical research, proteomics, and related fields.
Table of Content
Foreword vii
Preface ix
Contributors xi
About the Companion Website xvii
1 Biological Sequence Databases 1
Andreas D. Baxevanis
2 Information Retrieval from Biological Databases 19
Andreas D. Baxevanis
3 Assessing Pairwise Sequence Similarity: BLAST and FASTA 45
Andreas D. Baxevanis
4 Genome Browsers 79
Tyra G. Wolfsberg
5 Genome Annotation 117
David S. Wishart
6 Predictive Methods Using RNA Sequences 155
Michael F. Sloma, Michael Zuker, and David H. Mathews
7 Predictive Methods Using Protein Sequences 185
Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost
8 Multiple Sequence Alignments 227
Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins
9 Molecular Evolution and Phylogenetic Analysis 251
Emma J. Griffiths and Fiona S.L. Brinkman
10 Expression Analysis 279
Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush
11 Proteomics and Protein Identification by Mass Spectrometry 315
Sadhna Phanse and Andrew Emili
12 Protein Structure Prediction and Analysis 363
David S. Wishart
13 Biological Networks and Pathways 399
Gary D. Bader
14 Metabolomics 437
David S. Wishart
15 Population Genetics 481
Lynn B. Jorde and W. Scott Watkins
16 Metagenomics and Microbial Community Analysis 505
Robert G. Beiko
17 Translational Bioinformatics 537
Sean D. Mooney and Stephen J. Mooney
18 Statistical Methods for Biologists 555
Hunter N.B. Moseley
Appendices 583
Glossary 591
Index 609
About the author
EDITED BY
ANDREAS D. BAXEVANIS, Ph D, Director of Computational Biology for the National Institutes of Health’s Intramural Research Program and a Senior Scientist leading the Computational Genomics Unit at the NIH’s National Human Genome Research Institute, Bethesda, MD, USA.
GARY D. BADER, Ph D, Ontario Research Chair in Biomarkers of Disease and Professor at the Donnelly Centre and the Departments of Molecular Genetics and Computer Science at the University of Toronto, Toronto, ON, Canada.
DAVID S. WISHART, Ph D, Distinguished University Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta, Edmonton, AB, Canada.
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