Sequence Analysis in Molecular Biology

Preface

Chapter 1 Introduction: The Abnormalin Story

Chapter 2 The Collector's Dream: From Dayhoff to Data Banks

Chapter 3 Sequencing on the Computer: Programs That Make Lab Work Easier, Faster, and More Fun(?)

I. Designing Oligonucleotide Probes

II. Constructing Restriction Maps

III. Sequencing DNA

IV. Finding Restriction Sites

V. Translating DNA into Protein

VI. Simulating Cloning Experiments

Chapter 4 Nucleotide Sequences: What You Can Do With Your Sequence Once You Have It

I. Protein - DNA Interactions and Regulation of Gene Expression

II. Promoter Sequences

III. Terminator Sequences

IV. Splice Sites

V. Initiation of Protein Synthesis: Ribosome-Binding Sites

VI. Finding Coding Regions

VII. RNA Folding and Structure

VIII. DNA Geometry

Chapter 5 Protein Sequences: What You Can Do With Your Sequence Once You Have It

I. Rules of Protein Structure

II. Secondary Structure Prediction

III. Supersecondary Structure Prediction

IV. Predicting the Structural and Functional Class of a Protein

V. The Polar-Apolar Nature of Soluble and Membrane-Bound Proteins

VI. Sorting Signals in Proteins 1

VII. Covalent Modifications of Proteins

Chapter 6 Sequence Similarities, Homologies, and Alignments

I. Dot-Matrix Analysis

II. Global Alignments

III. Local Alignments

IV. Multiple Alignments

V. Measures of Amino Acid Similarity

VI. Estimating the Statistical Significance of an Alignment

Chapter 7 Machine Molecular Biology: Running Experiments on the Computer

I. Patterns That Were Not

II. Computer-Guided Intuition

Chapter 8 Sequences: Where Theoretical and Experimental Molecular Biology Meet

Appendix 1 Molecular Biology Databases

Appendix 2 Some Commercially Available Software Packages for Molecular Biology

Bibliography

Index