Introduction to Bioinformatics

ISBN-10: 1584885696
ISBN-13: 9781584885696
Edition: 2006
Authors: Anna Tramontano
List price: $79.95
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Description: 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  More...

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Book details

List price: $79.95
Copyright year: 2006
Publisher: CRC Press LLC
Publication date: 12/6/2006
Binding: Paperback
Pages: 192
Size: 6.00" wide x 9.25" long x 0.50" tall
Weight: 0.594
Language: English

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.

Anna Tramontano is Professor of Biochemistry at the Medical Faculty of the University of Rome "La Sapienza" since 2001. She received her PhD in Physics from the University of Naples (Italy) in 1980 and held various appointments at research institutes in Europe and in the U.S. before becoming Professor of Bioinformatics at the University of Milan in 1990. From 1996 to 2001 she held the position as director of Computational Biology and Chemistry at the Merck Research Laboratories in Rome. Anna Tramontano is among the organizers of the CASP (critical assessment of protein structure prediction) conferences and is on the editorial boards of several journals.

The Data: Storage and Retrieval
Glossary
Basic Principles
The Data
The Postgenomic Era
Nucleic Acid Data Banks
Protein Sequence Data Banks
Protein Structure Databases
Protein Interaction Databases
Derived Data Banks
Integration of Databases
Data Quality
Data Representation
Protein Architecture
References
Problems
Genome Sequence Analysis
Glossary
Basic Concepts
Genome Sequencing
Finding the Genes
Statistical Methods to Search for Genes
Site-Specific Scoring Matrices
Artificial Neural Networks
Markov Models and Hidden Markov Models
Levels of Reliability
Comparative Genomics
A Virtual Window on Genomes: The World Wide Web
References
Problems
Protein Evolution
Glossary
Basic Concepts
Molecular Evolution
How to Align Two Similar Sequences
Similarity Matrices
PAM Matrices
BLOSUM Matrices
Penalties for Insertions and Deletions
The Alignment Algorithm
Multiple Alignments
How to Add Sequences to a Pre-Existing Alignment
Phylogenetic Trees
References
Problems
Similarity Searches in Databases
Glossary
Basic Principles
The Methods
FASTA
Blast
Profile Searches
PSI-Blast
References
Problems
Amino Acid Sequence Analysis
Glossary
Basic Principles
Is It Really an Orphan Sequence?
Search for Sequence Patterns
Feature Extraction
Secondary Structure: Part One
References
Problems
Prediction of the Three-Dimensional Structure of a Protein
Glossary
Basic Principles
The CASP Experiment
Secondary Structure Prediction: Part Two
Long-Range Contact Prediction
Predicting Molecular Complexes: Docking Methods
References
Problems
Homology Modeling
Glossary
Basic Principles
The Steps of Comparative Modeling
Template Selection
Sequence Alignment
Loops
Side Chain Modeling
Model Optimization
Accuracy of Homology Models
Manual versus Automatic Models
Practical Notes
Summing Up
References
Problems
Fold Recognition Methods
Glossary
Basic Principles
Profile-Based Methods
Threading Methods
The Fold Library
How Well Do These Methods Work?
References
Problems
New Fold Modeling
Glossary
Basic Principles
Estimating the Energy of a Protein Conformation
Energy Minimization
Molecular Dynamics
The Monte Carlo Method
Genetic Algorithms
Combined Methodologies
References
Problems
The "Omics" Universe
Basic Principles
Transcriptomics
Proteomics
Interactomics
Structural Genomics
Pharmacogenomics
But This Is Not All
Useful Web Sites
Index

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