Developing Bioinformatics Computer Skills"O'Reilly Media, Inc.", 2001 - 427 頁 Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools. Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization. Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data. |
內容
Biology in the Computer Age | 3 |
How Is Computing Changing Biology? | 4 |
Isnt Bioinformatics Just About Building Databases? | 8 |
What Does Informatics Mean to Biologists? | 12 |
What Challenges Does Biology Offer Computer Scientists? | 13 |
Why Should Biologists Use Computers? | 14 |
How Can I Configure a PC to Do Bioinformatics Research? | 16 |
What Information and Software Are Available? | 18 |
The Chemistry of Proteins | 217 |
WebBased Protein Structure Tools | 229 |
Structure Visualization | 231 |
Structure Classification | 241 |
Structural Alignment | 247 |
Structure Analysis | 250 |
Solvent Accessibility and Interactions | 254 |
Computing Physicochemical Properties | 258 |
How Can I Use Web Information? | 19 |
How Do I Understand Sequence Alignment Data? | 20 |
How Do I Predict Protein Structure from Sequence? | 21 |
Computational Approaches to Biological Questions | 22 |
What Biologists Model | 27 |
Why Biologists Model | 31 |
Computational Methods Covered in This Book | 32 |
A Computational Biology Experiment | 38 |
The Bioinformatics Workstation | 45 |
Setting Up Your Workstation | 47 |
Setting Up a Linux Workstation | 50 |
How to Get Software Working | 56 |
What Software Is Needed? | 62 |
Files and Directories in Unix | 64 |
Working in a Multiuser Environment | 79 |
Working on a Unix System | 87 |
Issuing Commands on a Unix System | 89 |
Viewing and Editing Files | 94 |
Transformations and Filters | 101 |
File Statistics and Comparisons | 108 |
The Language of Regular Expressions | 110 |
Unix Shell Scripts | 113 |
Communicating with Other Computers | 114 |
Playing Nicely with Others in a Shared Environment | 119 |
Tools for Bioinformatics | 131 |
Biological Research on the Web | 133 |
Using Search Engines | 134 |
Finding Scientific Articles | 136 |
The Public Biological Databases | 140 |
Searching Biological Databases | 147 |
Depositing Data into the Public Databases | 155 |
Judging the Quality of Information | 156 |
Sequence Analysis Pairwise Alignment and Database Searching | 159 |
Chemical Composition of Biomolecules | 160 |
Composition of DNA and RNA | 161 |
Development of DNA Sequencing Methods | 164 |
Genefinders and Feature Detection in DNA | 169 |
DNA Translation | 171 |
Pairwise Sequence Comparison | 172 |
Sequence Queries Against Biological Databases | 182 |
Multifunctional Tools for Sequence Analysis | 188 |
Multiple Sequence Alignments Trees and Profiles | 191 |
Multiple Sequence Alignment | 193 |
Phylogenetic Analysis | 199 |
Profiles and Motifs | 205 |
Visualizing Protein Structures and Computing Structural Properties | 215 |
A Word About Protein Structure Data | 216 |
Structure Optimization | 260 |
Protein Resource Databases | 264 |
Putting It All Together | 265 |
Predicting Protein Structure and Function from Sequence | 268 |
Determining the Structures of Proteins | 269 |
Predicting the Structures of Proteins | 273 |
From 3D to ID | 275 |
Feature Detection in Protein Sequences | 276 |
Secondary Structure Prediction | 277 |
Predicting 3D Structure | 283 |
A Protein Modeling Project | 287 |
Summary | 293 |
Tools for Genomics and Proteomics | 294 |
From Sequencing Genes to Sequencing Genomes | 296 |
Sequence Assembly | 301 |
Accessing Genome Information on the Web | 303 |
Annotating and Analyzing Whole Genome Sequences | 307 |
New Data Analysis Challenges | 310 |
Proteomics | 317 |
Biochemical Pathway Databases | 321 |
Modeling Kinetics and Physiology | 325 |
Summary | 327 |
Databases and Visualization | 329 |
Automating Data Analysis with Perl | 331 |
Perl Basics | 332 |
Pattern Matching and Regular Expressions | 339 |
Parsing BLAST Output Using Perl | 340 |
Applying Perl to Bioinformatics | 345 |
Building Biological Databases | 350 |
Types of Databases | 351 |
Database Software | 359 |
Introduction to SQL | 361 |
Installing the MySQL DBMS | 366 |
Database Design | 371 |
Developing WebBased Software That Interacts with Databases | 375 |
Visualization and Data Mining | 383 |
Preparing Your Data | 384 |
Viewing Graphics | 385 |
Sequence Data Visualization | 386 |
Networks and Pathway Visualization | 388 |
Working with Numerical Data | 390 |
Summary | 396 |
Data Mining and Biological Information | 397 |
| 403 | |
| 409 | |