Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

BIOINFORMATICS SECOND EDITION......Page 3
CONTENTS......Page 9
Foreword......Page 15
Preface......Page 17
Contributors......Page 19
1 BIOINFORMATICS AND THE INTERNET......Page 21
Internet Basics......Page 22
Connecting to the Internet......Page 24
Electronic Mail......Page 27
File Transfer Protocol......Page 30
The World Wide Web......Page 33
Internet Resources for Topics Presented in Chapter 1......Page 36
References......Page 37
Introduction......Page 39
PUBs: Publications or Perish......Page 44
SEQ-Ids: What’s in a Name?......Page 48
BIOSEQs: Sequences......Page 51
BIOSEQ-SETs: Collections of Sequences......Page 54
SEQ-ANNOT: Annotating the Sequence......Page 55
SEQ-DESCR: Describing the Sequence......Page 60
Using the Model......Page 61
References......Page 63
Introduction......Page 65
Format vs. Content: Computers vs. Humans......Page 67
The GenBank Flatfile: A Dissection......Page 69
Internet Resources for Topics Presented in Chapter 3......Page 78
Appendix 3.1 Example of GenBank Flatfile Format......Page 79
Appendix 3.2 Example of EMBL Flatfile Format......Page 81
Appendix 3.3 Example of a Record in CON Division......Page 83
Introduction......Page 85
Why, Where, and What to Submit?......Page 86
DNA/RNA......Page 87
Protein-Only Submissions......Page 89
How to Submit with Sequin......Page 90
Consequences of the Data Model......Page 97
Concluding Remarks......Page 99
Internet Resources for Topics Presented in Chapter 4......Page 100
References......Page 101
Introduction to Structures......Page 103
PDB: Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB)......Page 107
MMDB: Molecular Modeling Database at NCBI......Page 111
Stucture File Formats......Page 114
Visualizing Structural Information......Page 115
Database Structure Viewers......Page 120
Structure Similarity Searching......Page 123
Internet Resources for Topics Presented in Chapter 5......Page 126
References......Page 127
6 GENOMIC MAPPING AND MAPPING DATABASES......Page 131
Interplay of Mapping and Sequencing......Page 132
Genomic Map Elements......Page 133
Types of Maps......Page 135
Complexities and Pitfalls of Mapping......Page 140
Data Repositories......Page 142
Mapping Projects and Associated Resources......Page 147
Practical Uses of Mapping Resources......Page 162
Internet Resources for Topics Presented in Chapter 6......Page 166
Problem Set......Page 168
References......Page 169
7 INFORMATION RETRIEVAL FROM BIOLOGICAL DATABASES......Page 175
Integrated Information Retrieval: The Entrez System......Page 176
LocusLink......Page 192
Sequence Databases Beyond NCBI......Page 198
Medical Databases......Page 201
Internet Resources for Topics Presented in Chapter 7......Page 203
Problem Set......Page 204
References......Page 205
Introduction......Page 207
The Evolutionary Basis of Sequence Alignment......Page 208
The Modular Nature of Proteins......Page 210
Optimal Alignment Methods......Page 213
Substitution Scores and Gap Penalties......Page 215
Database Similarity Searching......Page 218
FASTA......Page 220
BLAST......Page 222
Database Searching Artifacts......Page 224
Position-Specific Scoring Matrices......Page 228
Spliced Alignments......Page 229
Conclusions......Page 230
References......Page 232
Introduction......Page 235
Structural Alignment or Evolutionary Alignment?......Page 236
How to Multiply Align Sequences......Page 237
Tools to Assist the Analysis of Multiple Alignments......Page 242
Collections of Multiple Alignments......Page 247
Internet Resources for Topics Presented in Chapter 9......Page 248
Problem Set......Page 249
References......Page 250
10 PREDICTIVE METHODS USING DNA SEQUENCES......Page 253
GRAIL......Page 255
FGENEH/FGENES......Page 256
MZEF......Page 258
GENSCAN......Page 260
PROCRUSTES......Page 261
How Well Do the Methods Work?......Page 266
Strategies and Considerations......Page 268
Internet Resources for Topics Presented in Chapter 10......Page 270
References......Page 271
11 PREDICTIVE METHODS USING PROTEIN SEQUENCES......Page 273
Protein Identity Based on Composition......Page 274
Physical Properties Based on Sequence......Page 277
Motifs and Patterns......Page 279
Secondary Structure and Folding Classes......Page 283
Specialized Structures or Features......Page 289
Tertiary Structure......Page 294
Internet Resources for Topics Presented in Chapter 11......Page 297
Problem Set......Page 298
References......Page 299
12 EXPRESSED SEQUENCE TAGS (ESTs)......Page 303
What is an EST?......Page 304
EST Clustering......Page 308
STACK......Page 313
The Human Gene Map......Page 314
Gene Prediction in Genomic DNA......Page 315
Assessing Levels of Gene Expression Using ESTs......Page 316
Problem Set......Page 318
References......Page 319
13 SEQUENCE ASSEMBLY AND FINISHING METHODS......Page 323
The Use of Base Cell Accuracy Estimates or Confidence Values......Page 325
Global Assembly......Page 326
File Formats......Page 327
Preparing Readings for Assembly......Page 328
The Contig Selector......Page 331
The Contig Comparator......Page 332
The Template Display......Page 333
The Contig Editor......Page 336
Experiment Suggestion and Automation......Page 339
Internet Resources for Topics Presented in Chapter 13......Page 341
References......Page 342
14 PHYLOGENETIC ANALYSIS......Page 343
Fundamental Elements of Phylogenetic Models......Page 345
Phylogenetic Data Analysis: The Four Steps......Page 347
Alignment: Building the Data Model......Page 349
Alignment: Extraction of a Phylogenetic Data Set......Page 353
Determining the Substitution Model......Page 355
Tree-Building Methods......Page 360
Distance, Parsimony, and Maximum Likelihood: What’s the Difference?......Page 365
Tree Evaluation......Page 366
Phylogenetics Software......Page 368
Internet-Accessible Phylogenetic Analysis Software......Page 374
Internet Resources for Topics Presented in Chapter 14......Page 376
References......Page 377
15 COMPARATIVE GENOME ANALYSIS......Page 379
Progress in Genome Sequencing......Page 380
Genome Analysis and Annotation......Page 386
Application of Comparative Genomics—Reconstruction of Metabolic Pathways......Page 402
Avoiding Common Problems in Genome Annotation......Page 405
Internet Resources for Topics Presented in Chapter 15......Page 407
Problems for Additional Study......Page 409
References......Page 410
Introduction......Page 413
Technologies for Large-Scale Gene Expression......Page 414
Computational Tools for Expression Analysis......Page 419
Hierarchical Clustering......Page 427
Prospects for the Future......Page 429
References......Page 430
17 USING PERL TO FACILITATE BIOLOGICAL ANALYSIS......Page 433
Getting Started......Page 434
How Scripts Work......Page 436
Strings, Numbers, and Variables......Page 437
Arithmetic......Page 438
Variable Interpolation......Page 439
Basic Input and Output......Page 440
Filehandles......Page 442
Making Decisions......Page 444
Conditional Blocks......Page 447
Loops......Page 450
Combining Loops with Input......Page 452
Standard Input and Output......Page 453
Finding the Length of a Sequence File......Page 455
Pattern Matching......Page 456
Extracting Patterns......Page 460
Arrays......Page 461
Split and Join......Page 464
Hashes......Page 465
A Real-World Example......Page 466
Suggested Reading......Page 469
Glossary......Page 471
Index......Page 477