Muutke küpsiste eelistusi

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 2nd Revised edition [Kõva köide]

3.63/5 (19 hinnangut Goodreads-ist)
(University of British Columbia, Canada), Edited by , , Edited by ,
  • Formaat: Hardback, 488 pages, kõrgus x laius: 260x186 mm, kaal: 1106 g, Ill.
  • Sari: Methods of Biochemical Analysis
  • Ilmumisaeg: 04-May-2001
  • Kirjastus: John Wiley & Sons Inc
  • ISBN-10: 0471383902
  • ISBN-13: 9780471383901
Teised raamatud teemal:
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 2nd Revised editionSuurem pilt
  • Formaat: Hardback, 488 pages, kõrgus x laius: 260x186 mm, kaal: 1106 g, Ill.
  • Sari: Methods of Biochemical Analysis
  • Ilmumisaeg: 04-May-2001
  • Kirjastus: John Wiley & Sons Inc
  • ISBN-10: 0471383902
  • ISBN-13: 9780471383901
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9780471383901.html
Märksõnad:
Many of the contributors are from the Center for Biotechnology Information at the US National Institutes of Health, and others are scientists and instructors from around North America and Britain. Their work can be used as a classroom text, a tutorial, or a laboratory bench reference. No date is noted for the first edition, but the second reinforces concepts that have survived from the first, and incorporates new approaches and algorithms for analyzing genes and proteins. New chapters discuss expressed sequence tags, sequence assembly, comparative genomics, large-scale genome analysis, and BioPerl. Answers to the problems are available on a web site. Annotation c. Book News, Inc., Portland, OR (booknews.com)
Foreword xiii Preface xv Contributors xvii Bioinformatics and the Internet 1(18) Andreas D. Baxevanis Internet Basics 2(2) Connecting to the Internet 4(3) Electronic Mail 7(3) File Transfer Protocol 10(3) The World Wide Web 13(3) Internet Resources for Topics Presented in
Chapter 1 16(1) References 17(2) The NCBI Data Model 19(26) James M. Ostell Sarah J. Wheelan Jonathan A. Kans Introduction 19(5) PUBs: Publications or Perish 24(4) SEQ-Ids: Whats in a Name? 28(3) BIOSEQs: Sequences 31(3) BIOSEQ-SETs: Collections of Sequences 34(1) SEQ-ANNOT: Annotating the Sequence 35(5) SEQ-DESCR: Describing the Sequence 40(1) Using the Model 41(2) Conclusions 43(1) References 43(2) The Genbank Sequence Database 45(20) Ilene Karsch-Mizrachi B. F. Francis Ouellette Introduction 45(2) Primary and Secondary Databases 47(1) Format vs. Content: Computers vs. Humans 47(2) The Database 49(1) The GenBank Flatfile: A Dissection 49(9) Concluding Remarks 58(1) Internet Resources for Topics Presented in
Chapter 3 58(1) References 59(1) Appendices 59(6) Appendix 3.1 Example of GenBank Flatfile Format 59(2) Appendix 3.2 Example of EMBL Flatfile Format 61(2) Appendix 3.3 Example of a Record in CON Division 63(2) Submitting DNA Sequences to the Databases 65(18) Jonathan A. Kans B. F. Francis Ouellette Introduction 65(1) Why, Where, and What to Submit? 66(1) DNA/RNA 67(2) Population, Phylogenetic, and Mutation Studies 69(1) Protein-Only Submissions 69(1) How to Submit on the World Wide Web 70(1) How to Submit with Sequin 70(7) Updates 77(1) Consequences of the Data Model 77(2) EST/STS/GSS/HTG/SNP and Genome Centers 79(1) Concluding Remarks 79(1) Contact Points for Submission of Sequence Data to DDBJ/EMBL/GenBank 80(1) Internet Resources for Topics Presented in
Chapter 4 80(1) References 81(2) Structure Databases 83(28) Christopher W. V. Hogue Introduction to Structures 83(4) PDB: Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB) 87(4) MMDB: Molecular Modeling Database at NCBI 91(3) Stucture File Formats 94(1) Visualizing Structural Information 95(5) Database Structure Viewers 100(3) Advanced Structure Modeling 103(1) Structure Similarity Searching 103(3) Internet Resources for Topics Presented in
Chapter 5 106(1) Problem Set 107(1) References 107(4) Genomic Mapping And Mapping Databases 111(44) Peter S. White Tara C. Matise Interplay of Mapping and Sequencing 112(1) Genomic Map Elements 113(2) Types of Maps 115(5) Complexities and Pitfalls of Mapping 120(2) Data Repositories 122(5) Mapping Projects and Associated Resources 127(15) Practical Uses of Mapping Resources 142(4) Internet Resources for Topics Presented in
Chapter 6 146(2) Problem Set 148(1) References 149(6) Information Retrieval From Biological Databases 155(32) Andreas D. Baxevanis Integrated Information Retrieval: The Entrez System 156(16) LocusLink 172(6) Sequence Databases Beyond NCBI 178(3) Medical Databases 181(2) Internet Resources for Topics Presented in
Chapter 7 183(1) Problem Set 184(1) References 185(2) Sequence Alignment and Database Searching 187(28) Gregory D. Schuler Introduction 187(1) The Evolutionary Basis of Sequence Alignment 188(2) The Modular Nature of Proteins 190(3) Optimal Alignment Methods 193(2) Substitution Scores and Gap Penalties 195(3) Statistical Significance of Alignments 198(1) Database Similarity Searching 198(2) FASTA 200(2) BLAST 202(2) Database Searching Artifacts 204(4) Position-Specific Scoring Matrices 208(1) Spliced Alignments 209(1) Conclusions 210(2) Internet Resources for Topics Presented in
Chapter 8 212(1) References 212(3) Creation and Analysis of Protein Multiple Sequence Alignments 215(18) Geoffrey J. Barton Introduction 215(1) What is a Multiple Alignment, and Why Do It? 216(1) Structural Alignment or Evolutionary Alignment? 216(1) How to Multiply Align Sequences 217(5) Tools to Assist the Analysis of Multiple Alignments 222(5) Collections of Multiple Alignments 227(1) Internet Resources for Topics Presented in
Chapter 9 228(1) Problem Set 229(1) References 230(3) Predictive Methods Using DNA Sequences 233(20) Andreas D. Baxevanis GRAIL 235(1) Fgeneh/Fgenes 236(2) MZEF 238(2) GENSCAN 240(1) POCRUSTES 241(5) How Well Do the Methods Work? 246(2) Strategies and Considerations 248(2) Internet Resources for Topics Presented in
Chapter 10 250(1) Problem Set 251(1) References 251(2) Predictive Methods Using Protein Sequences 253(30) Sharmila Banerjee-Basu Andreas D. Baxevanis Protein Identity Based on Composition 254(3) Physical Properties Based on Sequence 257(2) Motifs and Patterns 259(4) Secondary Structure and Folding Classes 263(6) Specialized Structures or Features 269(5) Tertiary Structure 274(3) Internet Resources for Topics Presented in
Chapter 11 277(1) Problem Set 278(1) References 279(4) Expressed Sequence Tags (ESTs) 283(20) Tyra G. Wolfsberg David Landsman What is an EST? 284(4) EST Clustering 288(5) TIGR Gene Indices 293(1) STACK 293(1) ESTs and Gene Discovery 294(1) The Human Gene Map 294(1) Gene Prediction in Genomic DNA 295(1) ESTs and Sequence Polymorphisms 296(1) Assessing Levels of Gene Expression Using ESTs 296(2) Internet Resources for Topics Presented in
Chapter 12 298(1) Problem Set 298(1) References 299(4) Sequence Assembly and Finishing Methods 303(20) Rodger Staden David P. Judge James K. Bonfield The Use of Base Cell Accuracy Estimates or Confidence Values 305(1) The Requirements for Assembly Software 306(1) Global Assembly 306(1) File Formats 307(1) Preparing Readings for Assembly 308(3) Introduction to Gap4 311(1) The Contig Selector 311(1) The Contig Comparator 312(1) The Template Display 313(3) The Consistency Display 316(1) The Contig Editor 316(3) The Contig Joining Editor 319(1) Disassembling Readings 319(1) Experiment Suggestion and Automation 319(2) Concluding Remarks 321(1) Internet Resources for Topics Presented in
Chapter 13 321(1) Problem Set 322(1) References 322(1) Phylogenetic Analysis 323(36) Fiona S. L. Brinkman Detlef D. Leipe Fundamental Elements of Phylogenetic Models 325(2) Tree Interpretation---The Importance of Identifying Paralogs and Orthologs 327(1) Phylogenetic Data Analysis: The Four Steps 327(2) Alignment: Building the Data Model 329(4) Alignment: Extraction of a Phylogenetic Data Set 333(2) Determining the Substitution Model 335(5) Tree-Building Methods 340(5) Distance, Parsimony, and Maximum Likelihood: Whats the Difference? 345(1) Tree Evaluation 346(2) Phylogenetics Software 348(6) Internet-Accessible Phylogenetic Analysis Software 354(2) Some Simple Practical Considerations 356(1) Internet Resources for Topics Presented in
Chapter 14 356(1) References 357(2) Comparative Genome Analysis 359(34) Michael Y. Galperin Eugene V. Koonin Progress in Genome Sequencing 360(6) Genome Analysis and Annotation 366(16) Application of Comparative Genomics---Reconstruction of Metabolic Pathways 382(3) Avoiding Common Problems in Genome Annotation 385(2) Conclusions 387(1) Internet Resources for Topics Presented in
Chapter 15 387(2) Problems for Additional Study 389(1) References 390(3) Large-Scale Genome Analysis 393(20) Paul S. Meltzer Introduction 393(1) Technologies for Large-Scale Gene Expression 394(5) Computational Tools for Expression Analysis 399(8) Hierarchical Clustering 407(2) Prospects for the Future 409(1) Internet Resources for Topics Presented in
Chapter 16 410(1) References 410(3) Using Perl to Facilitate Biological Analysis 413(38) Lincoln D. Stein Getting Started 414(2) How Scripts Work 416(1) Strings, Numbers, and Variables 417(1) Arithmetic 418(1) Variable Interpolation 419(1) Basic Input and Output 420(2) Filehandles 422(2) Making Decisions 424(3) Conditional Blocks 427(3) What is Truth? 430(1) Loops 430(2) Combining Loops with Input 432(1) Standard Input and Output 433(2) Finding the Length of a Sequence File 435(1) Pattern Matching 436(4) Extracting Patterns 440(1) Arrays 441(3) Arrays and Lists 444(1) Split and Join 444(1) Hashes 445(1) A Real-World Example 446(3) Where to Go From Here 449(1) Internet Resources for Topics Presented in
Chapter 17 449(1) Suggested Reading 449(2) Glossary 451(6) Index 457