Essential Bioinformatics

ISBN-10: 0521600820

ISBN-13: 9780521600828

Edition: 2006

Authors: Jin Xiong
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Description: Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

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Book details

List price: $84.99
Copyright year: 2006
Publisher: Cambridge University Press
Publication date: 3/13/2006
Binding: Paperback
Pages: 352
Size: 6.75" wide x 9.75" long x 0.75" tall
Weight: 1.870
Language: English

Jin Xiong is Assistant Professor of Biology at Texas A & M University, where he has taught bioinformatics to graduate and undergraduate students for several years.

Preface
Introduction and Biological Databases
Introduction
What Is Bioinformatics?
Goal
Scope
Applications
Limitations
New Themes
Further Reading
Introduction to Biological Databases
What Is a Database?
Types of Databases
Biological Databases
Pitfalls of Biological Databases
Information Retrieval from Biological Databases
Summary
Further Reading
Sequence Alignment
Pairwise Sequence Alignment
Evolutionary Basis
Sequence Homology versus Sequence Similarity
Sequence Similarity versus Sequence Identity
Methods
Scoring Matrices
Statistical Significance of Sequence Alignment
Summary
Further Reading
Database Similarity Searching
Unique Requirements of Database Searching
Heuristic Database Searching
Basic Local Alignment Search Tool (BLAST)
FASTA
Comparison of FASTA and BLAST
Database Searching with the Smith-Waterman Method
Summary
Further Reading
Multiple Sequence Alignment
Scoring Function
Exhaustive Algorithms
Heuristic Algorithms
Practical Issues
Summary
Further Reading
Profiles and Hidden Markov Models
Position-Specific Scoring Matrices
Profiles
Markov Model and Hidden Markov Model
Summary
Further Reading
Protein Motifs and Domain Prediction
Identification of Motifs and Domains in Multiple Sequence Alignment
Motif and Domain Databases Using Regular Expressions
Motif and Domain Databases Using Statistical Models
Protein Family Databases
Motif Discovery in Unaligned Sequences
Sequence Logos
Summary
Further Reading
Gene and Promoter Prediction
Gene Prediction
Categories of Gene Prediction Programs
Gene Prediction in Prokaryotes
Gene Prediction in Eukaryotes
Summary
Further Reading
Promoter and Regulatory Element Prediction
Promoter and Regulatory Elements in Prokaryotes
Promoter and Regulatory Elements in Eukaryotes
Prediction Algorithms
Summary
Further Reading
Molecular Phylogenetics
Phylogenetics Basics
Molecular Evolution and Molecular Phylogenetics
Terminology
Gene Phylogeny versus Species Phylogeny
Forms of Tree Representation
Why Finding a True Tree Is Difficult
Procedure
Summary
Further Reading
Phylogenetic Tree Construction Methods and Programs
Distance-Based Methods
Character-Based Methods
Phylogenetic Tree Evaluation
Phylogenetic Programs
Summary
Further Reading
Structural Bioinformatics
Protein Structure Basics
Amino Acids
Peptide Formation
Dihedral Angles
Hierarchy
Secondary Structures
Tertiary Structures
Determination of Protein Three-Dimensional Structure
Protein Structure Database
Summary
Further Reading
Protein Structure Visualization, Comparison, and Classification
Protein Structural Visualization
Protein Structure Comparison
Protein Structure Classification
Summary
Further Reading
Protein Secondary Structure Prediction
Secondary Structure Prediction for Globular Proteins
Secondary Structure Prediction for Transmembrane Proteins
Coiled Coil Prediction
Summary
Further Reading
Protein Tertiary Structure Prediction
Methods
Homology Modeling
Threading and Fold Recognition
Ab Initio Protein Structural Prediction
CASP
Summary
Further Reading
RNA Structure Prediction
Introduction
Types of RNA Structures
RNA Secondary Structure Prediction Methods
Ab Initio Approach
Comparative Approach
Performance Evaluation
Summary
Further Reading
Genomics and Proteomics
Genome Mapping, Assembly, and Comparison
Genome Mapping
Genome Sequencing
Genome Sequence Assembly
Genome Annotation
Comparative Genomics
Summary
Further Reading
Functional Genomics
Sequence-Based Approaches
Microarray-Based Approaches
Comparison of SAGE and DNA Microarrays
Summary
Further Reading
Proteomics
Technology of Protein Expression Analysis
Posttranslational Modification
Protein Sorting
Protein-Protein Interactions
Summary
Further Reading
Appendix
Practical Exercises
Glossary
Index
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