Sequence Analysis Primer

by Gribskov, Michael; Devereux, John

• ISBN13: 9780195098747
• ISBN10: 0195098749
• Edition: Revised
• Format: Paperback
• Copyright: 1993-09-23
• Publisher: Oxford University Press

Summary

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 Biography

Michael Gribskov, Ph.D., is Principle Scientist at the San Diego Superconductor Center and Adjunct Assistant Professor of Biology at the University of California, San Diego John Devereux, Ph.D., is President of Genetics Computer Group, Inc.

Table of Contents

Foreword	p. xiii
DNA
Sequencing Project Management	p. 1
Getting Started	p. 1
Choosing a Software Package	p. 1
Sequence Reading Hardware	p. 2
Creating a Database	p. 5
Project Standards	p. 5
Sequence Entry and Quality Control	p. 6
Sequence Entry	p. 6
Sequence Checking	p. 7
Removing Vector Sequence	p. 7
Restriction Site Checking	p. 8
Sequence Assembly	p. 8
Finding Overlaps and Building Contigs	p. 8
Confirming Overlaps	p. 10
Shotgun Projects	p. 13
Progressive Deletions	p. 13
Walking Primers	p. 14
The Last Few Gaps	p. 14
Error Detection and Correction	p. 17
Incorrect Overlaps	p. 17
Progress Reports	p. 18
Open Reading Frames and Other Traps	p. 20
The Final Result	p. 23
Identification of Simple Sites and Transcriptional Signals	p. 23
Sequence Patterns	p. 23
Pattern Matching Programs	p. 24
Restriction Enzymes	p. 26
Restriction Enzyme Databases	p. 26
Searching for Fixed Patterns	p. 26
Promoters and Enhancers	p. 27
Bacterial Promoters	p. 28
Eukaryotic Promoters	p. 29
Enhancers and Transcription Factors	p. 31
Terminators and Attenuators	p. 32
Coding Region Identification	p. 32
Identification of mRNA Signals	p. 35
Ribosome Binding Sites	p. 35
The Initiation Codon	p. 36
The Stop Codon	p. 39
Suppressor tRNAs	p. 39
RNA Splice Sites	p. 39
Polyadenylation Signals	p. 42
Coding Region Sequence Patterns	p. 43
Base Composition Bias	p. 44
TestCode Analysis	p. 44
Codon Bias	p. 45
Correspondence Analysis	p. 48
Codon Usage and Gene Expression Prediction	p. 48
Assembly of Continuous Coding Sequences	p. 49
RNA Structure	p. 49
Optimal Folding	p. 51
Suboptimal Folding	p. 53
Pseudoknots	p. 53
Interactive Folding	p. 54
Representation of Folded Structures	p. 55
DNA Structure	p. 56
Identification of Stem and Loop Regions	p. 57
DNA Conformation	p. 57
Summary	p. 58
Protein
Physical Properties	p. 61
Molecular Weight and Amino Acid Composition	p. 61
Isoelectric Point and Extinction Coefficient	p. 63
Structural Properties	p. 64
Secondary Structure Prediction	p. 64
Hydrophobicity Patterns	p. 67
Detection of the Outside Face of Helices	p. 77
Detection of Motifs	p. 78
Post-translational Modification Sites	p. 82
Supersecondary Structure	p. 83
Folding Domain Motifs	p. 84
Sequence Families	p. 85
Summary	p. 86
Similarity and Homology
Similarity versus Homology	p. 90
Dot Matrix Methods	p. 92
Algorithms	p. 93
The Simple Dot Plot	p. 93
The Window Approach and Output Filtering	p. 97
Estimation of Statistical Significance	p. 100
Examples	p. 105
Gene and Genome Structure and Evolution	p. 105
RNA and DNA Structure and Folding	p. 106
Protein Sequence Organization and Comparison	p. 106
Analysis of Repetitive Sequence Proteins	p. 109
Summary and Future Developments	p. 124
Dynamic Programming Methods	p. 124
Derivation of Dynamic Programming Alignment	p. 125
Simple Example of Dynamic Programming Alignment	p. 127
More Complicated Alignments	p. 130
Other Derivations	p. 132
Extensions	p. 134
Scoring Systems	p. 134
Fast Methods	p. 137
Hashing and Neighborhood Algorithms	p. 138
Finite State Machines	p. 140
Statistical Approaches - BLAST	p. 140
Multiple Sequence Alignment	p. 141
Extension of Pairwise Alignment Techniques	p. 144
Data Interdependence and Sequence Weighting	p. 145
Examples of Multiple Sequence Alignment	p. 146
Multiple Alignment for Database Searching	p. 147
Similarity and Significance	p. 148
Theoretical Foundations of Molecular Evolution	p. 148
Statistical Analysis of Alignments	p. 152
Examples	p. 154
Summary	p. 157
Practical Aspects: Analysis of Notch
Background	p. 159
Strategy	p. 160
cDNA Sequence Analysis	p. 160
Sequencing Project Management	p. 160
Restriction Map	p. 163
Finding Open Reading Frames	p. 164
Codon Preference	p. 164
TestCode Statistic	p. 165
Windows	p. 169
Protein Analysis: Determining Structure and Function	p. 169
Database Searches	p. 169
FASTA	p. 170
Scan for Motifs with PROSITE	p. 173
BLAST	p. 177
Aligning Notch and Xotch	p. 179
The Algorithm	p. 179
Looking for Internal Repeats	p. 184
Dotplot	p. 184
Aligning the Repeated Regions	p. 187
Profile Analysis	p. 190
Hydropathy Plot	p. 191
Transmembrane Region?	p. 192
Antigenic Determinants	p. 193
Secondary Structure	p. 194
Protein Degradation: PEST Sequences	p. 195
Genomic DNA	p. 196
Weight Matrices	p. 196
Simple Regulatory Elements	p. 197
RNA Stem and Loop Structures	p. 200
Summary	p. 201
References	p. 205
Appendices
Nucleic Acid Codes	p. 225
Amino Acid Codes and Properties	p. 227
Amino Acid Composition of Proteins in PIR Release 26	p. 229
Log-odds Matrices	p. 231
A Partial List of Software Suppliers	p. 235
Hardware	p. 239
Electronic Communication	p. 243
Sequence and Structural Databases	p. 259
Data Submission	p. 263
Glossary	p. 271
Index	p. 277
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