6.4 Searching Biological Databases_____________________________________________________ 131
6.5 Depositing Data into the Public Databases__________________________________________________ 138
6.6 Finding Software ____________________________________________________________________ 138
6.7 Judging the Quality of Information _______________________________________________________ 139
Chapter 7. Sequence Analysis, Pairwise Alignment, and Database Searching ____________________142
7.1 Chemical Composition of Biomolecules ___________________________________________________ 143
7.2 Composition of DNA and RNA ______________________________________________________ 143
7.3 Watson and Crick Solve the Structure of DNA _________________________________________ 144
7.4 Development of DNA Sequencing Methods ___________________________________________ 146
7.5 Genefinders and Feature Detection in DNA _________________________________________________ 149
7.6 DNA Translation __________________________________________________________________ 151
7.7 Pairwise Sequence Comparison_____________________________________________________ 152
7.8 Sequence Queries Against Biological Databases ______________________________________ 160
7.9 Multifunctional Tools for Sequence Analysis ________________________________________________ 167
Chapter 8. Multiple Sequence Alignments, Trees, and Profiles ________________________________169
8.1 The Morphological to the Molecular ______________________________________________________ 169
8.2 Multiple Sequence Alignment _______________________________________________________ 170
8.3 Phylogenetic Analysis _____________________________________________________________ 175
8.4 Profiles and Motifs ________________________________________________________________ 180
Chapter 9. Visualizing Protein Structures and Computing Structural Properties _________________189
9.1 A Word About Protein Structure Data _____________________________________________________ 189
9.2 The Chemistry of Proteins __________________________________________________________ 190
9.3 Web-Based Protein Structure Tools__________________________________________________ 201
9.4 Structure Visualization _____________________________________________________________ 202
9.5 Structure Classification ____________________________________________________________ 210
9.6 Structural Alignment_______________________________________________________________ 215
9.7 Structure Analysis ___________________________________________________________________ 218
9.8 Solvent Accessibility and Interactions________________________________________________ 221
9.9 Computing Physicochemical Properties ____________________________________________________ 224
9.10 Structure Optimization ____________________________________________________________ 226
9.11 Protein Resource Databases____________________________________________________________ 229
9.12 Putting It All Together_____________________________________________________________ 230
Chapter 10. Predicting Protein Structure and Function from Sequence _________________________232
10.1 Determining the Structures of Proteins ______________________________________________ 232
10.2 Predicting the Structures of Proteins _____________________________________________________ 236
10.3 From 3D to 1D_____________________________________________________________________ 237
10.4 Feature Detection in Protein Sequences ___________________________________________________ 238
10.5 Secondary Structure Prediction ____________________________________________________ 239
10.6 Predicting 3D Structure ___________________________________________________________ 243
10.7 Putting It All Together: A Protein Modeling Project ____________________________________ 247
10.8 Summary _______________________________________________________________________ 252
Chapter 11. Tools for Genomics and Proteomics ____________________________________________253
11.1 From Sequencing Genes to Sequencing Genomes ____________________________________ 254
11.2 Sequence Assembly ______________________________________________________________ 258
11.3 Accessing Genome Informationon the Web __________________________________________ 259
11.4 Annotating and Analyzing Whole Genome Sequences ________________________________________ 263
11.5 Functional Genomics: New Data Analysis Challenges _________________________________ 265
11.6 Proteomics ______________________________________________________________________ 270
11.7 Biochemical Pathway Databases ___________________________________________________ 274
11.8 Modeling Kinetics and Physiology_______________________________________________________ 277
11.9 Summary _______________________________________________________________________ 278
Chapter 12. Automating Data Analysis with Perl ____________________________________________280
12.1 Why Perl? ________________________________________________________________________ 280
12.2 Perl Basics ________________________________________________________________________ 281
12.3 Pattern Matching and Regular Expressions_________________________________________________ 286
