Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins [Kõva köide]

Preface vii(7) Contributors xiv 1 The Internet and the Biologist 1(15) Andreas D. Baxevanis Internet Basics 1(2) Connecting to the Internet 3(1) Electronic Mail 4(3) File Transfer Protocol 7(1) Gopher 8(1) The World Wide Web 8(7) References 15(1) 2 The GenBank Sequence Database 16(30) B. F. Francis Ouellette Introduction 16(3) Primary and Secondary Databases 19(1) Format vs. Content: Computers vs. Humans 20(1) The Database 21(1) The GenBank Flatfile: A Dissection 22(11) Conclusions 33(1) References 33(2) Appendices: Database File Formats 35(11) Appendix 2.1 Example of an GenBank (or DDBS) Record 35(1) Appendix 2.2 Example of an ASN.1 Record 36(6) Appendix 2.3 Example of an EMBL Record 42(2) Appendix 2.4 Example of a GenBank Summary File 44(2) 3 Structure Databases 46(28) Christopher W. V. Hogue Stephen H. Bryant Introduction to Structures 46(3) PDB: Protein Data Bank at Brookhaven National Laboratories 49(7) MMDB: Molecular Modeling Database at NCBI 56(2) Structure File Formats 58(2) Visualizing Structural Information 60(8) Database Structure Viewers 68(2) Cant Find a Published Structure? 70(1) References 71(1) Monographs 72(2) 4 Sequence Analysis Using GCG 74(24) Barbara A. Butler Introduction 74(1) The Wisconsin Package 75(1) Database That Accompany the Wisconsin Package 75(1) The SeqLab Environment 76(4) Analyzing Sequences with Operations and Wisconsin Package Programs 80(1) Viewing Output 81(2) Monitoring Program Progress and Troubleshooting Problems 83(1) Annotating Sequences and Graphically Displaying Annotations in the SeqLab Editor 83(2) Saving Sequences in the SeqLab Editor 85(1) Examples of Analyses That Can Be Undertaken in SeqLab 85(6) Extending SeqLab by Including Programs That Are Not Part of the Wisconsin Package 91(1) References 91(2) Appendix 93(5) 5 Information Retrieval from Biological Databases 98(23) Andreas D. Baxevanis Retrieving Database Entries: The Retrieve Server 99(2) Integrated Information Retrieval: The Entrez System 101(10) Integrated Information Access: The Query Server 111(4) Sequence Databases Beyond NCBI 115(3) Medical Databases 118(2) References 120(1) 6 The NCBI Data Model 121(24) James M. Ostell Jonathan A. Kans Introduction 121(4) Pubs: Publications or Perish 125(4) Seqids: Whats in a Name? 129(3) Bioseq: Sequences 132(3) BioseqSets: Collections of Sequences 135(1) Seq-annot: Annotating the Sequence 136(4) Seq-descr: Describing the Sequence 140(1) Using the Model 141(2) Conclusions 143(1) References 144(1) 7 Sequence Alignment and Database Searching 145(27) Gregory D. Schuler Introduction 145(1) The Evolutionary Basis of Sequence Alignment 146(2) The Modular Nature of Proteins 148(2) Optimal Alignment Methods 150(1) Substitution Scores and Gap Penalties 151(4) Statistical Significance of Alignments 155(1) Database Similarity Searching 156(3) FASTA 159(1) BLAST 160(6) Low-Complexity Regions 166(1) Repetitive Elements 166(3) Conclusions 169(1) References 170(2) 8 Practical Aspects of Multiple Sequence Alignment 172(17) Andreas D. Baxevanis Progressive Alignment Methods 173(3) Motifs and Patterns 176(8) Presentation Methods 184(4) References 188(1) 9 Phylogenetic Analysis 189(42) Mark A. Hershkovitz Detlef D. Leipe Elements of Phylogenetic Models 190(1) Phylogenetic Data Analysis: Alignment, Substitution Model Building, Tree Building, and Tree Evaluation 191(1) Building the Data Model (Alignment) 191(6) Determining the Substitution Model 197(9) Tree-Building Methods 206(5) Searching for Trees 211(1) Rooting Trees 212(1) Evaluating Trees and Data 213(4) Phylogenetics Software 217(8) Some Simple Practical Considerations 225(2) Acknowledgments 227(1) References 227(4) 10 Predictive Methods Using Nucleotide Sequences 231(15) James W. Fickett Framework 232(1) Masking Repetitive DNA 232(2) Database Searches 234(1) Codon Bias Detection 234(2) Detecting Functional Sites in the DNA 236(2) Integrated Gene Parsing 238(1) Finding tRNA Genes 238(3) Future Prospects 241(2) Acknowledgments 243(1) References 243(3) 11 Predictive Methods Using Protein Sequences 246(22) Andreas D. Baxevanis David Landsman Protein Identity Based on Composition 247(3) Physical Properties Based on Sequence 250(2) Secondary Structure and Folding Classes 252(5) Specialized Structures or Features 257(5) Tertiary Structure 262(3) References 265(3) 12 Of Mice and Men: Navigating Public Physical Mapping Databases 268(31) Lincoln D. Stein Types of Physical Map 269(2) Genome-Wide Maps from Large Community Databases 271(7) Genome-Wide Maps from Individual Sources 278(13) Chromosome-Specific Human Maps 291(3) Mouse Mapping Resources 294(3) References 297(2) 13 ACEDB: A Database for Genome Information 299(20) Sean Walsh Mary Anderson Samuel W. Cartinhour General Features of ACEDB 299(6) Sequence Analysis in ACEDB 305(10) Miscellaneous Analysis Functions 315(1) Acknowledgments 316(3) 14 Submitting DNA Sequence to the Databases 319(36) Jonathan A. Kans B. F. Francis Ouellette Introduction 319(1) Where to Submit? 320(1) What to Submit? 321(3) How to Submit on the World Wide Web 324(2) How to Submit with Sequin 326(22) EST/STS/GSS 348(1) Genome Centers 348(2) Updates 350(1) Concluding Remarks 351(1) Acknowledgments 351(2) References 353(2) Appendix 1: Glossary 355(4) Appendix 2: Sample Sequence File Formats 359(4) Index 363