EDITED BY ANDREAS D. BAXEVANIS, PhD, 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, PhD, 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, PhD, Distinguished University Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta, Edmonton, AB, Canada.

• Foreword viiPreface ixContributors xiAbout the Companion Website xvii1 Biological Sequence Databases 1Andreas D. Baxevanis2 Information Retrieval from Biological Databases 19Andreas D. Baxevanis3 Assessing Pairwise Sequence Similarity: BLAST and FASTA 45Andreas D. Baxevanis4 Genome Browsers 79Tyra G. Wolfsberg5 Genome Annotation 117David S. Wishart6 Predictive Methods Using RNA Sequences 155Michael F. Sloma, Michael Zuker, and David H. Mathews7 Predictive Methods Using Protein Sequences 185Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost8 Multiple Sequence Alignments 227Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins9 Molecular Evolution and Phylogenetic Analysis 251Emma J. Griffiths and Fiona S.L. Brinkman10 Expression Analysis 279Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush11 Proteomics and Protein Identification by Mass Spectrometry 315Sadhna Phanse and Andrew Emili12 Protein Structure Prediction and Analysis 363David S. Wishart13 Biological Networks and Pathways 399Gary D. Bader14 Metabolomics 437David S. Wishart15 Population Genetics 481Lynn B. Jorde and W. Scott Watkins16 Metagenomics and Microbial Community Analysis 505Robert G. Beiko17 Translational Bioinformatics 537Sean D. Mooney and Stephen J. Mooney18 Statistical Methods for Biologists 555Hunter N.B. MoseleyAppendices 583Glossary 591Index 609

EDITED BY ANDREAS D. BAXEVANIS, PhD, 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, PhD, 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, PhD, Distinguished University Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta, Edmonton, AB, Canada.

• Foreword viiPreface ixContributors xiAbout the Companion Website xvii1 Biological Sequence Databases 1Andreas D. Baxevanis2 Information Retrieval from Biological Databases 19Andreas D. Baxevanis3 Assessing Pairwise Sequence Similarity: BLAST and FASTA 45Andreas D. Baxevanis4 Genome Browsers 79Tyra G. Wolfsberg5 Genome Annotation 117David S. Wishart6 Predictive Methods Using RNA Sequences 155Michael F. Sloma, Michael Zuker, and David H. Mathews7 Predictive Methods Using Protein Sequences 185Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost8 Multiple Sequence Alignments 227Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins9 Molecular Evolution and Phylogenetic Analysis 251Emma J. Griffiths and Fiona S.L. Brinkman10 Expression Analysis 279Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush11 Proteomics and Protein Identification by Mass Spectrometry 315Sadhna Phanse and Andrew Emili12 Protein Structure Prediction and Analysis 363David S. Wishart13 Biological Networks and Pathways 399Gary D. Bader14 Metabolomics 437David S. Wishart15 Population Genetics 481Lynn B. Jorde and W. Scott Watkins16 Metagenomics and Microbial Community Analysis 505Robert G. Beiko17 Translational Bioinformatics 537Sean D. Mooney and Stephen J. Mooney18 Statistical Methods for Biologists 555Hunter N.B. MoseleyAppendices 583Glossary 591Index 609

EDITED BY ANDREAS D. BAXEVANIS, PhD, 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, PhD, 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, PhD, Distinguished University Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta, Edmonton, AB, Canada.

• Foreword viiPreface ixContributors xiAbout the Companion Website xvii1 Biological Sequence Databases 1Andreas D. Baxevanis2 Information Retrieval from Biological Databases 19Andreas D. Baxevanis3 Assessing Pairwise Sequence Similarity: BLAST and FASTA 45Andreas D. Baxevanis4 Genome Browsers 79Tyra G. Wolfsberg5 Genome Annotation 117David S. Wishart6 Predictive Methods Using RNA Sequences 155Michael F. Sloma, Michael Zuker, and David H. Mathews7 Predictive Methods Using Protein Sequences 185Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost8 Multiple Sequence Alignments 227Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins9 Molecular Evolution and Phylogenetic Analysis 251Emma J. Griffiths and Fiona S.L. Brinkman10 Expression Analysis 279Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush11 Proteomics and Protein Identification by Mass Spectrometry 315Sadhna Phanse and Andrew Emili12 Protein Structure Prediction and Analysis 363David S. Wishart13 Biological Networks and Pathways 399Gary D. Bader14 Metabolomics 437David S. Wishart15 Population Genetics 481Lynn B. Jorde and W. Scott Watkins16 Metagenomics and Microbial Community Analysis 505Robert G. Beiko17 Translational Bioinformatics 537Sean D. Mooney and Stephen J. Mooney18 Statistical Methods for Biologists 555Hunter N.B. MoseleyAppendices 583Glossary 591Index 609