1  Cover

      2  Foreword

      3  Preface

      4  Contributors

      5  About the Companion Website

      6  1 Biological Sequence Databases Introduction Nucleotide Sequence Databases Nucleotide Sequence Flatfiles: A Dissection Protein Sequence Databases Summary Acknowledgments Internet Resources Further Reading References

      7  2 Information Retrieval from Biological Databases Introduction Integrated Information Retrieval: The Entrez System Medical Databases Organismal Sequence Databases Beyond NCBI Summary Further Reading References

      8  3 Assessing Pairwise Sequence Similarity: BLAST and FASTA Introduction Global Versus Local Sequence Alignments Scoring Matrices BLAST BLAST 2 Sequences MegaBLAST PSI-BLAST BLAT FASTA Summary Further Reading References

      9  4 Genome Browsers Introduction The UCSC Genome Browser UCSC Table Browser ENSEMBL Genome Browser Ensembl Biomart JBrowse Summary Further Reading References

      10  5 Genome Annotation Introduction Gene Prediction Methods Ab Initio Gene Prediction in Prokaryotic Genomes Ab Initio Gene Prediction in Eukaryotic Genomes How Well Do Gene Predictors Work? Assessing Prokaryotic Gene Predictors Assessing Eukaryotic Gene Predictors Evidence Generation for Genome Annotation Gene Annotation and Evidence Generation using Comparative Gene Prediction Genome Annotation Pipelines Summary Acknowledgments Internet Resources Further Reading References

      11  6 Predictive Methods Using RNA Sequences Introduction Overview of RNA Secondary Structure Prediction Using Thermodynamics Dynamic Programming Accuracy of RNA Secondary Structure Prediction Predicting the Secondary Structure Common to Multiple RNA Sequences Practical Introduction to Single-Sequence Methods Practical Introduction to Multiple Sequence Methods Other Computational Methods to Study RNA Structure Comparison of Methods Predicting RNA Tertiary Structure Summary Further Reading