Foreword vii // Preface ix // Contributors xi // About the Companion Website xvii // Biological Sequence Databases 1 - Andreas D. Baxevanis // Information Retrieval from Biological Databases 19 - Andreas D. Baxevanis // Assessing Pairwise Sequence Similarity: BLAST and FASTA 45 - Andreas D. Baxevanis // Genome Browsers 79 - Tyra G. Wolfsberg // Genome Annotation 117 - David S. Wishart // Predictive Methods Using RNA Sequences 155 - MichaeL F. Sioma, Michael Zuker, and David H. Mathews // Predictive Methods Using Protein Sequences 185 - Jonas Reeb, Tatyana Goldberg, Yanay Ofran, and Burkhard Rost // Multiple Sequence Alignments 227 - Fabian Sievers, Geoffrey J. Barton, and Desmond G. Higgins // Molecular Evolution and Phylogenetic Analysis 251 - Emma J. Griffiths and Fiona S.L. Brinkman // Expression Analysis 279 - Marieke L. Kuijjer, Joseph N. Paulson, and John Quackenbush // Proteomics and Protein Identification by Mass Spectrometry 315 - Sadhna Phonse and Andrew Emili // Protein Structure Prediction and Analysis 363 - David S. Wishart // 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