Table of Contents
Foreword vii
Preface ix
Contributors xi
About the Companion Website xvii
1 Biological Sequence Databases 1Andreas D. Baxevanis
2 Information Retrieval from Biological Databases 19Andreas D. Baxevanis
3 Assessing Pairwise Sequence Similarity: BLAST and FASTA 45Andreas D. Baxevanis
4 Genome Browsers 79Tyra G. Wolfsberg
5 Genome Annotation 117David S. Wishart
6 Predictive Methods Using RNA Sequences 155Michael F. Sloma, Michael Zuker, and David H. Mathews
7 Predictive Methods Using Protein Sequences 185Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost
8 Multiple Sequence Alignments 227Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins
9 Molecular Evolution and Phylogenetic Analysis 251Emma J. Griffiths and Fiona S.L. Brinkman
10 Expression Analysis 279Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush
11 Proteomics and Protein Identification by Mass Spectrometry 315Sadhna Phanse and Andrew Emili
12 Protein Structure Prediction and Analysis 363David S. Wishart
13 Biological Networks and Pathways 399Gary D. Bader
14 Metabolomics 437David S. Wishart
15 Population Genetics 481Lynn B. Jorde and W. Scott Watkins
16 Metagenomics and Microbial Community Analysis 505Robert G. Beiko
17 Translational Bioinformatics 537Sean D. Mooney and Stephen J. Mooney
18 Statistical Methods for Biologists 555Hunter N.B. Moseley
Appendices 583
Glossary 591
Index 609