Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the beginner the necessary background to enter this vital field and helps more seasoned researchers to fine-tune their approach. It covers basic data manipulation such as homology searches, stem-loop identification, and protein secondary structure prediction, and is compatible with most sequence analysis programs. A detailed example giving steps for characterizing a new gene sequence provides users with hands-on experience when combined with their current software. The book will be invaluable to researchers and students in molecular biology, genetics, biochemistry, microbiology, and biotechnology.
Author(s): Michael Gribskov, John Devereux
Year: 1993
Language: English
Pages: 296
Contents......Page 8
Foreword......Page 14
Getting Started......Page 18
Sequence Entry and Quality Control......Page 23
Sequence Assembly......Page 25
Error Detection and Correction......Page 34
Sequence Patterns......Page 40
Pattern Matching Programs......Page 41
Restriction Enzymes......Page 43
Promoters and Enhancers......Page 44
Coding Region Identification......Page 49
Identification of mRNA Signals......Page 52
Coding Region Sequence Patterns......Page 60
RNA Structure......Page 66
Optimal Folding......Page 68
Pseudoknots......Page 70
Interactive Folding......Page 71
Representation of Folded Structures......Page 72
DNA Structure......Page 73
DNA Conformation......Page 74
Summary......Page 75
Molecular Weight and Amino Acid Composition......Page 78
Isoelectric Point and Extinction Coefficient......Page 80
Secondary Structure Prediction......Page 81
Hydrophobicity Patterns......Page 84
Detection of the Outside Face of Helices......Page 94
Detection of Motifs......Page 95
Summary......Page 103
3 Similarity and Homology......Page 106
Similarity versus Homology......Page 107
Dot Matrix Methods......Page 109
Algorithms......Page 110
Examples......Page 122
Dynamic Programming Methods......Page 141
Derivation of Dynamic Programming Alignment......Page 142
More Complicated Alignments......Page 147
Other Derivations......Page 149
Scoring Systems......Page 151
Fast Methods......Page 154
Hashing and Neighborhood Algorithms......Page 155
Statistical Approaches - BLAST......Page 157
Multiple Sequence Alignment......Page 158
Extension of Pairwise Alignment Techniques......Page 161
Data Interdependence and Sequence Weighting......Page 162
Examples of Multiple Sequence Alignment......Page 163
Multiple Alignment for Database Searching......Page 164
Theoretical Foundations of Molecular Evolution......Page 165
Statistical Analysis of Alignments......Page 169
Examples......Page 171
Summary......Page 174
Background......Page 176
Sequencing Project Management......Page 177
Restriction Map......Page 180
Finding Open Reading Frames......Page 181
Database Searches......Page 186
Aligning Notch and Xotch......Page 196
Looking for Internal Repeats......Page 201
Profile Analysis......Page 207
Hydropathy Plot......Page 208
Secondary Structure......Page 211
Protein Degradation: PEST Sequences......Page 212
Weight Matrices......Page 213
RNA Stem and Loop Structures......Page 217
Summary......Page 218
References......Page 222
Appendices......Page 240
I. Nucleic Acid Codes......Page 242
II. Amino Acid Codes and Properties......Page 244
III. Amino Acid Composition of Proteins in PIR Release 26......Page 246
IV. Log-odds Matrices......Page 248
V. A Partial List of Software Suppliers......Page 252
VI. Hardware......Page 256
VII. Electronic Communication......Page 260
VIII. Sequence and Structural Databases......Page 276
IX. Data Submission......Page 280
C......Page 288
G......Page 289
L......Page 290
P......Page 291
W......Page 292
Z......Page 293
D......Page 294
P......Page 295
W......Page 296
