Bioinformatics Sequence and Genome Analysis

cover......Page 1
Historical Introduction and Overview......Page 2
THE FIRST SEQUENCES TO BE COLLECTED WERE THOSE OF PROTEINS......Page 3
DNA SEQUENCE DATABASES......Page 4
SEQUENCE RETRIEVAL FROM PUBLIC DATABASES......Page 5
THE DOT MATRIX OR DIAGRAM METHOD FOR COMPARING SEQUENCES......Page 6
ALIGNMENT OF SEQUENCES BY DYNAMIC PROGRAMMING......Page 7
FINDING LOCAL ALIGNMENTS BETWEEN SEQUENCES......Page 9
PREDICTION OF RNA SECONDARY STRUCTURE......Page 10
DISCOVERY OF EVOLUTIONARY RELATIONSHIPS USING SEQUENCES......Page 11
THE FASTA AND BLAST METHODS FOR DATABASE SEARCHES......Page 12
PREDICTING THE SEQUENCE OF A PROTEIN BY TRANSLATION OF DNA SEQUENCES......Page 13
PREDICTING PROTEIN SECONDARY STRUCTURE......Page 14
THE FIRST COMPLETE GENOME SEQUENCE......Page 15
REFERENCES......Page 16
Collecting and Storing Sequences in
the Laboratory......Page 20
DNA sequencing,......Page 21
SEQUENCING cDNA LIBRARIES OF EXPRESSED GENES......Page 26
SEQUENCE ACCURACY......Page 27
SEQUENCE FORMATS......Page 30
CONVERSIONS OF ONE SEQUENCE FORMAT TO ANOTHER......Page 37
MULTIPLE SEQUENCE FORMATS......Page 41
STORAGE OF INFORMATION IN A SEQUENCE DATABASE......Page 45
USING THE DATABASE ACCESS PROGRAM ENTREZ......Page 46
REFERENCES......Page 49
Alignment of Pairs of Sequences......Page 52
DEFINITION OF SEQUENCE ALIGNMENT......Page 54
Significance of sequence alignment,......Page 55
Overview of methods of sequence alignment,......Page 57
METHODS,......Page 59
REFERENCES,......Page 135
Multiple Sequence Alignment......Page 140
INTRODUCTION......Page 141
USES OF MULTIPLE SEQUENCE ALIGNMENTS......Page 143
RELATIONSHIP OF MULTIPLE SEQUENCE ALIGNMENT TO PHYLOGENETIC ANALYSIS......Page 144
METHODS......Page 145
MULTIPLE SEQUENCE ALIGNMENT AS AN EXTENSION OF SEQUENCE PAIR
ALIGNMENT BY DYNAMIC PROGRAMMING......Page 146
SCORING MULTIPLE SEQUENCE ALIGNMENTS......Page 152
PROGRESSIVE METHODS OF MULTIPLE SEQUENCE ALIGNMENT......Page 153
OTHER PROGRAMS AND METHODS FOR MULTIPLE SEQUENCE ALIGNMENT......Page 161
LOCALIZED ALIGNMENTS IN SEQUENCES......Page 162
STATISTICAL METHODS FOR AIDING ALIGNMENT......Page 174
POSITION-SPECIFIC SCORING MATRICES......Page 193
MULTIPLE SEQUENCE ALIGNMENT EDITORS AND FORMATTERS......Page 199
REFERENCES......Page 201
Prediction of RNA
Secondary Structure......Page 206
INTRODUCTION......Page 207
FEATURES OF RNA SECONDARY STRUCTURE......Page 209
LIMITATIONS OF PREDICTION......Page 211
DEVELOPMENT OF RNA PREDICTION METHODS......Page 212
SELF-COMPLEMENTARY REGIONS IN RNA SEQUENCES PREDICT SECONDARY
STRUCTURE......Page 213
MINIMUM FREE-ENERGY METHOD FOR RNA SECONDARY STRUCTURE
PREDICTION......Page 215
SUBOPTIMAL STRUCTURE PREDICTIONS BY MFOLD AND THE USE
OF ENERGY PLOTS......Page 216
OTHER ALGORITHMS FOR SUBOPTIMAL FOLDING OF RNA MOLECULES......Page 218
PREDICTION OF MOST PROBABLE RNA SECONDARY STRUCTURE......Page 220
USING SEQUENCE COVARIATION TO PREDICT STRUCTURE......Page 224
STOCHASTIC CONTEXT-FREE GRAMMARS FOR MODELING
RNA SECONDARY STRUCTURE......Page 229
SEARCHING GENOMES FOR RNA-SPECIFYING GENES......Page 231
APPLICATIONS OF RNA STRUCTURE MODELING......Page 233
REFERENCES......Page 234
Phylogenetic Prediction......Page 238
INTRODUCTION......Page 239
RELATIONSHIP OF PHYLOGENETIC ANALYSIS TO SEQUENCE ALIGNMENT......Page 240
GENOME COMPLEXITY AND PHYLOGENETIC ANALYSIS......Page 241
THE CONCEPT OF EVOLUTIONARY TREES......Page 245
METHODS......Page 248
MAXIMUM PARSIMONY METHOD......Page 249
DISTANCE METHODS......Page 255
THE MAXIMUM LIKELIHOOD APPROACH......Page 275
SEQUENCE ALIGNMENT BASED ON AN EVOLUTIONARY MODEL......Page 276
COMPLICATIONS FROM PHYLOGENETIC ANALYSIS......Page 279
REFERENCES......Page 280
Database Searching for
Similar Sequences......Page 282
INTRODUCTION......Page 283
ALLOWING FAST SEARCHES......Page 284
DNA VERSUS PROTEIN SEARCHES......Page 287
SCORING MATRICES FOR SIMILARITY SEARCHES......Page 289
LIMITING OUTPUT......Page 290
METHODS......Page 291
FASTA SEQUENCE DATABASE SIMILARITY SEARCH......Page 292
BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST)......Page 301
DATABASE SEARCHES WITH THE SMITH-WATERMAN
DYNAMIC PROGRAMMING METHOD......Page 316
DATABASE SEARCHES WITH THE BAYES BLOCK ALIGNER......Page 318
DATABASE SEARCHES WITH A SCORING MATRIX OR PROFILE......Page 321
SEARCHING SEQUENCE DATABASES WITH A POSITION-SPECIFIC
SCORING MATRIX OR SEQUENCE PROFILE......Page 322
OTHER METHODS FOR COMPARING DATABASES OF SEQUENCES AND PATTERNS......Page 327
SUMMARY......Page 333
REFERENCES......Page 335
Gene Prediction......Page 338
INTRODUCTION......Page 339
TESTING THE RELIABILITY OF AN ORF PREDICTION......Page 343
EUKARYOTIC GENES HAVE REPEATED SEQUENCE ELEMENTS THAT PROBABLY
REFLECT NUCLEOSOME STRUCTURE......Page 344
METHODS......Page 347
GENE PREDICTION IN MICROBIAL GENOMES......Page 349
GENE PREDICTION IN EUKARYOTES......Page 353
EVALUATION OF GENE PREDICTION METHODS......Page 357
PROMOTER PREDICTION IN E. COLI......Page 358
PROMOTER PREDICTION IN EUKARYOTES......Page 367
REFERENCES......Page 374
Protein Classification and
Structure Prediction......Page 382
PROTEIN STRUCTURE PREDICTION......Page 383
REVIEW OF PROTEIN STRUCTURE AND TERMINOLOGY......Page 387
PROTEIN CLASSIFICATION......Page 390
METHODS......Page 399
VIEWING PROTEIN STRUCTURES......Page 401
PROTEIN STRUCTURE CLASSIFICATION DATABASES......Page 403
ALIGNMENT OF PROTEIN STRUCTURES......Page 404
STRUCTURAL PREDICTION......Page 428
EVALUATING THE SUCCESS OF STRUCTURE PREDICTIONS......Page 472
STRUCTURAL MODELING......Page 473
REFERENCES......Page 474
Genome Analysis......Page 480
INTRODUCTION......Page 481
GENOME ANATOMY......Page 482
SEQUENCE ASSEMBLY AND GENE IDENTIFICATION......Page 492
METHODS......Page 493
COMPARATIVE GENOMICS......Page 501
FUNCTIONAL CLASSIFICATION OF GENES......Page 510
GENE ORDER (SYNTENY) IS CONSERVED ON CHROMOSOMES OF RELATED
ORGANISMS......Page 511
GLOBAL GENE REGULATION......Page 520
PREDICTION OF GENE FUNCTION BASED ON A COMPOSITE ANALYSIS......Page 524
PUTTING TOGETHER ALL OF THE INFORMATION INTO A GENOME DATABASE......Page 526
REFERENCES......Page 528
Glossary......Page 534
Index......Page 548