Introduction to Bioinformatics

ISBN-13: 9781584885696 / Angielski / Miękka / 2006 / 192 str.

Anna Tramontano

Opis

Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems.

Spis treści

The Data: Storage and Retrieval
Basic Principles
The Data
Data Quality
Data Representation
Genome Sequence Analysis
Basic Concepts
Genome Sequencing
Finding the Genes
Statistical Methods to Search for Genes
Comparative Genomics
A Virtual Window on Genomes: The World Wide Web
Protein Evolution
Basic Concepts
Molecular Evolution
How to Align Two Similar Sequences
Similarity Matrices
Penalties for Insertions and Deletions
The Alignment Algorithm
Multiple Alignments
Phylogenetic Trees
Similarity Searches in Databases
Basic Principles
The Methods
Amino Acid Sequence Analysis
Basic Principles
Search for Sequence Patterns
Feature Extraction
Secondary Structure: Part One
Prediction of the Three-Dimensional Structure of a Protein
Basic Principles
The CASP Experiment
Secondary Structure Prediction: Part Two
Long-Range Contact Prediction
Predicting Molecular Complexes: Docking Methods
Homology Modeling
Basic Principles
The Steps of Comparative Modeling
Accuracy of Homology Models
Manual versus Automatic Models
Practical Notes
Summing Up
Fold Recognition Methods
Basic Principles
Profile-Based Methods
Threading Methods
The Fold Library
How Well Do These Methods Work?
New Fold Modeling
Basic Principles
Estimating the Energy of a Protein Conformation
Energy Minimization
Molecular Dynamics
The “Omics” Universe
Basic Principles
Transcriptomics
Proteomics
Interactomics
Structural Genomics
Pharmacogenomics
But This Is Not All
Useful Web Sites
Index
A Glossary, References, and Problems appear in each chapter.

O autorze

Anna Tramontano