Developing Bioinformatics Computer Skills

封面
"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.

 

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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
Bibliography
403
Index
409
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關於作者 (2001)

Cynthia Gibas is an assistant professor of biology at Virginia Tech, in Blacksburg, Virginia. She's been a computational biologist since before computational biology was cool, and is currently learning to drive her spankin' new home-built Linux cluster. Her research interests include the structure and evolution of genomes, the properties of protein surfaces and interfaces, and prediction of protein structure. She teaches introductory courses in bioinformatics methods for biologists and is looking forward to her next real vacation, sometime in 2006.

Per Jambeck is a Ph.D. student in the bioengineering department at the University of California, San Diego. He has worked on computational biology problems since 1994, concentrating on machine learning applications in understanding multidimensional biological data. Per smiles wistfully at the mention of free time, but he manages to host shows at community and student-run radio stations anyway.

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