Bioinformatics: a practical guide to the analysis of genes and proteins

Y L F M A E T Team-Fly® BIOINFORMATICS SECOND EDITION METHODSOF BIOCHEMICALANALYSIS Volume43 BIOINFORMATICS A Practical Guide to the Analysis of Genes and Proteins SECOND EDITION Andreas D. Baxevanis Genome Technology Branch National Human Genome Research Institute National Institutes of Health Bethesda, Maryland USA B. F. Francis Ouellette Centre for Molecular Medicine and Therapeutics Children’s and Women’s Health Centre of British Columbia University of British Columbia Vancouver, British Columbia Canada A JOHN WILEY & SONS, INC., PUBLICATION New York • Chichester • Weinheim • Brisbane • Singapore • Toronto Designationsusedbycompaniestodistinguishtheirproductsareoftenclaimedastrademarks.Inallinstances whereJohnWiley&Sons,Inc.,isawareofaclaim,theproductnamesappearininitialcapitalorALLCAPITAL LETTERS.Readers,however,shouldcontacttheappropriatecompaniesformorecompleteinformationregarding trademarksandregistration. Copyright(cid:1)2001byJohnWiley&Sons,Inc.Allrightsreserved. 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ADB dedicates this book to his Goddaughter, Anne Terzian, for her constant kindness, good humor, and love—and for always making me smile. BFFO dedicates this book to his daughter, Maya. Her sheer joy and delight in the simplest of things lights up my world everyday. CONTENTS Foreword ........................................................................................ xiii Preface ........................................................................................... xv Contributors ................................................................................... xvii 1 BIOINFORMATICS AND THE INTERNET 1 Andreas D. Baxevanis Internet Basics .......................................................................... 2 Connecting to the Internet .......................................................... 4 Electronic Mail ......................................................................... 7 File Transfer Protocol ................................................................ 10 The World Wide Web ................................................................ 13 Internet Resources for Topics Presented in Chapter 1 .................... 16 References ................................................................................ 17 2 THE NCBI DATA MODEL 19 James M. Ostell, Sarah J. Wheelan, and Jonathan A. Kans Introduction .............................................................................. 19 PUBs: Publications or Perish ...................................................... 24 SEQ-Ids: What’s in a Name? ...................................................... 28 BIOSEQs: Sequences ................................................................. 31 BIOSEQ-SETs: Collections of Sequences ..................................... 34 SEQ-ANNOT:Annotating the Sequence ...................................... 35 SEQ-DESCR: Describing the Sequence ....................................... 40 Using the Model ....................................................................... 41 Conclusions .............................................................................. 43 References ................................................................................ 43 3 THE GENBANK SEQUENCE DATABASE 45 Ilene Karsch-Mizrachi and B. F. Francis Ouellette Introduction .............................................................................. 45 Primary and Secondary Databases ............................................... 47 Format vs. Content: Computers vs. Humans ................................. 47 The Database ............................................................................ 49 vii viii CONTENTS The GenBank Flat?le:A Dissection ............................................. 49 Concluding Remarks .................................................................. 58 Internet Resources for Topics Presented in Chapter 3 .................... 58 References ................................................................................ 59 Appendices ............................................................................... 59 Appendix 3.1 Example of GenBank Flat?le Format .................. 59 Appendix 3.2 Example of EMBL Flat?le Format ...................... 61 Appendix 3.3 Example of a Record in CON Division ............... 63 4 SUBMITTING DNA SEQUENCES TO THE DATABASES 65 Jonathan A. Kans and B. F. Francis Ouellette Introduction .............................................................................. 65 Why, Where, and What to Submit? ............................................. 66 DNA/RNA ................................................................................ 67 Population, Phylogenetic, and Mutation Studies ............................ 69 Protein-Only Submissions ........................................................... 69 How to Submit on the World Wide Web ...................................... 70 How to Submit with Sequin ....................................................... 70 Updates .................................................................................... 77 Consequences of the Data Model ................................................ 77 EST/STS/GSS/HTG/SNPand Genome Centers ............................. 79 Concluding Remarks .................................................................. 79 Contact Points for Submission of Sequence Data to DDBJ/EMBL/GenBank ........................................................... 80 Internet Resources for Topics Presented in Chapter 4 .................... 80 References ................................................................................ 81 5 STRUCTURE DATABASES 83 Christopher W. V. Hogue Introduction to Structures ........................................................... 83 PDB: Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB) ............................................ 87 MMDB: Molecular Modeling Database at NCBI .......................... 91 Stucture File Formats ................................................................. 94 Visualizing Structural Information ............................................... 95 Database Structure Viewers ........................................................ 100 Advanced Structure Modeling ..................................................... 103 Structure Similarity Searching ..................................................... 103 Internet Resources for Topics Presented in Chapter 5 .................... 106 Problem Set .............................................................................. 107 References ................................................................................ 107 6 GENOMIC MAPPING AND MAPPING DATABASES 111 Peter S. White and Tara C. Matise Interplay of Mapping and Sequencing ......................................... 112 Genomic Map Elements ............................................................. 113 CONTENTS ix Types of Maps .......................................................................... 115 Complexities and Pitfalls of Mapping .......................................... 120 Data Repositories ...................................................................... 122 Mapping Projects and Associated Resources ................................. 127 Practical Uses of Mapping Resources .......................................... 142 Internet Resources for Topics Presented in Chapter 6 .................... 146 Problem Set .............................................................................. 148 References ................................................................................ 149 7 INFORMATION RETRIEVAL FROM BIOLOGICAL DATABASES 155 Andreas D. Baxevanis Integrated Information Retrieval: The Entrez System ..................... 156 LocusLink ................................................................................ 172 Sequence Databases Beyond NCBI ............................................. 178 Medical Databases ..................................................................... 181 Internet Resources for Topics Presented in Chapter 7 .................... 183 Problem Set .............................................................................. 184 References ................................................................................ 185 8 SEQUENCE ALIGNMENT AND DATABASE SEARCHING 187 Gregory D. Schuler Introduction .............................................................................. 187 The Evolutionary Basis of Sequence Alignment ............................ 188 The Modular Nature of Proteins .................................................. 190 OptimalAlignment Methods ....................................................... 193 Substitution Scores and Gap Penalties ......................................... 195 Statistical Signi?cance of Alignments .......................................... 198 Database Similarity Searching ..................................................... 198 FASTA ..................................................................................... 200 BLAST .................................................................................... 202 Database SearchingArtifacts ....................................................... 204 Position-Speci?c Scoring Matrices .............................................. 208 SplicedAlignments .................................................................... 209 Conclusions .............................................................................. 210 Internet Resources for Topics Presented in Chapter 8 .................... 212 References ................................................................................ 212 9 CREATION AND ANALYSIS OF PROTEIN MULTIPLE SEQUENCE ALIGNMENTS 215 Geoffrey J. Barton Introduction .............................................................................. 215 What is a MultipleAlignment, and Why Do It? ........................... 216 StructuralAlignment or EvolutionaryAlignment? ......................... 216 How to MultiplyAlign Sequences ............................................... 217