Bioinformatics: Sequence and Genome Analysis

✍ Scribed by David W. Mount

• Publisher: Cold Spring Harbor Laboratory
• Year: 2001
• Tongue: English
• Leaves: 573
• Edition: 1
• Category: Library

✦ Synopsis

The application of computational methods to DNA and protein science is the newest and most exciting new development in biology. "Bioinformatics: Sequence and Genome Analysis" is a comprehensive functional and theoretical introduction to this new discipline. Sequence alignment, structure prediction, phylogenetic and gene prediction, database searching, and genome analysis are amply explained and illustrated. Descriptions, instructions, and web references are provided for a broad range of publicly available software. Links to online resources, problems for classroom use, and additional material not included in the text are available on the book’s own website, that will be updated as the field moves on.

Based on the author’s extensive teaching experience at the University of Arizona, this is a uniquely educational book, ideal for investigators, graduate students, and biology undergraduates studying this new, fast-changing discipline, and also for computer programmers and information specialists working in molecular biology and pharmaceutical laboratories.

✦ Table of Contents

Cover
Pre-title
Title
Copyright
The Bioinformatics Web Site
Contents
Historical Introduction and Overview
THE FIRST SEQUENCES TO BE COLLECTED WERE THOSE OF PROTEINS
DNA SEQUENCE DATABASES
SEQUENCE RETRIEVAL FROM PUBLIC DATABASES
SEQUENCE ANALYSIS PROGRAMS
THE DOT MATRIX OR DIAGRAM METHOD FOR COMPARING SEQUENCES
ALIGNMENT OF SEQUENCES BY DYNAMIC PROGRAMMING
FINDING LOCAL ALIGNMENTS BETWEEN SEQUENCES
MULTIPLE SEQUENCE ALIGNMENT
PREDICTION OF RNA SECONDARY STRUCTURE
DISCOVERY OF EVOLUTIONARY RELATIONSHIPS USING SEQUENCES
IMPORTANCE OF DATABASE SEARCHES FOR SIMILAR SEQUENCES
THE FASTA AND BLAST METHODS FOR DATABASE SEARCHES
PREDICTING THE SEQUENCE OF A PROTEIN BY TRANSLATION OF DNA SEQUENCES
PREDICTING PROTEIN SECONDARY STRUCTURE
THE FIRST COMPLETE GENOME SEQUENCE
ACEDB, THE FIRST GENOME DATABASE
REFERENCES
Collecting and Storing Sequences in the Laboratory
DNA sequencing,
SEQUENCING cDNA LIBRARIES OF EXPRESSED GENES
SUBMISSION OF SEQUENCES TO THE DATABASES
SEQUENCE ACCURACY
SEQUENCE FORMATS
CONVERSIONS OF ONE SEQUENCE FORMAT TO ANOTHER
MULTIPLE SEQUENCE FORMATS
STORAGE OF INFORMATION IN A SEQUENCE DATABASE
USING THE DATABASE ACCESS PROGRAM ENTREZ
REFERENCES
Alignment of Pairs of Sequences
INTRODUCTION
DEFINITION OF SEQUENCE ALIGNMENT
Significance of sequence alignment,
Overview of methods of sequence alignment,
METHODS,
REFERENCES,
Multiple Sequence Alignment
INTRODUCTION
GENOME SEQUENCING
USES OF MULTIPLE SEQUENCE ALIGNMENTS
RELATIONSHIP OF MULTIPLE SEQUENCE ALIGNMENT TO PHYLOGENETIC ANALYSIS
METHODS
MULTIPLE SEQUENCE ALIGNMENT AS AN EXTENSION OF SEQUENCE PAIR ALIGNMENT BY DYNAMIC PROGRAMMING
SCORING MULTIPLE SEQUENCE ALIGNMENTS
PROGRESSIVE METHODS OF MULTIPLE SEQUENCE ALIGNMENT
OTHER PROGRAMS AND METHODS FOR MULTIPLE SEQUENCE ALIGNMENT
LOCALIZED ALIGNMENTS IN SEQUENCES
STATISTICAL METHODS FOR AIDING ALIGNMENT
POSITION-SPECIFIC SCORING MATRICES
MULTIPLE SEQUENCE ALIGNMENT EDITORS AND FORMATTERS
REFERENCES
Prediction of RNA Secondary Structure
INTRODUCTION
RNA STRUCTURE PREDICTION BASICS
FEATURES OF RNA SECONDARY STRUCTURE
LIMITATIONS OF PREDICTION
DEVELOPMENT OF RNA PREDICTION METHODS
METHODS
SELF-COMPLEMENTARY REGIONS IN RNA SEQUENCES PREDICT SECONDARY STRUCTURE
MINIMUM FREE-ENERGY METHOD FOR RNA SECONDARY STRUCTURE PREDICTION
SUBOPTIMAL STRUCTURE PREDICTIONS BY MFOLD AND THE USE OF ENERGY PLOTS
OTHER ALGORITHMS FOR SUBOPTIMAL FOLDING OF RNA MOLECULES
PREDICTION OF MOST PROBABLE RNA SECONDARY STRUCTURE
USING SEQUENCE COVARIATION TO PREDICT STRUCTURE
STOCHASTIC CONTEXT-FREE GRAMMARS FOR MODELING RNA SECONDARY STRUCTURE
SEARCHING GENOMES FOR RNA-SPECIFYING GENES
APPLICATIONS OF RNA STRUCTURE MODELING
REFERENCES
Phylogenetic Prediction
INTRODUCTION
RELATIONSHIP OF PHYLOGENETIC ANALYSIS TO SEQUENCE ALIGNMENT
GENOME COMPLEXITY AND PHYLOGENETIC ANALYSIS
THE CONCEPT OF EVOLUTIONARY TREES
METHODS
MAXIMUM PARSIMONY METHOD
DISTANCE METHODS
THE MAXIMUM LIKELIHOOD APPROACH
SEQUENCE ALIGNMENT BASED ON AN EVOLUTIONARY MODEL
RELIABILITY OF PHYLOGENETIC PREDICTIONS
COMPLICATIONS FROM PHYLOGENETIC ANALYSIS
REFERENCES
Database Searching for Similar Sequences
INTRODUCTION
SEQUENCE SIMILARITY SEARCH WITH A SINGLE QUERY SEQUENCE
ALLOWING FAST SEARCHES
DNA VERSUS PROTEIN SEARCHES
SCORING MATRICES FOR SIMILARITY SEARCHES
LIMITING OUTPUT
METHODS
FASTA SEQUENCE DATABASE SIMILARITY SEARCH
BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST)
DATABASE SEARCHES WITH THE SMITH-WATERMAN DYNAMIC PROGRAMMING METHOD
DATABASE SEARCHES WITH THE BAYES BLOCK ALIGNER
DATABASE SEARCHES WITH A SCORING MATRIX OR PROFILE
SEARCHING SEQUENCE DATABASES WITH A POSITION-SPECIFIC SCORING MATRIX OR SEQUENCE PROFILE
OTHER METHODS FOR COMPARING DATABASES OF SEQUENCES AND PATTERNS
SUMMARY
REFERENCES
Gene Prediction
INTRODUCTION
TESTING THE RELIABILITY OF AN ORF PREDICTION
EUKARYOTIC GENES HAVE REPEATED SEQUENCE ELEMENTS THAT PROBABLY REFLECT NUCLEOSOME STRUCTURE
METHODS
GENE PREDICTION IN MICROBIAL GENOMES
GENE PREDICTION IN EUKARYOTES
EVALUATION OF GENE PREDICTION METHODS
PROMOTER PREDICTION IN E. COLI
PROMOTER PREDICTION IN EUKARYOTES
REFERENCES
Protein Classification and Structure Prediction
INTRODUCTION
PROTEIN STRUCTURE PREDICTION
REVIEW OF PROTEIN STRUCTURE AND TERMINOLOGY
PROTEIN CLASSIFICATION
METHODS
VIEWING PROTEIN STRUCTURES
PROTEIN STRUCTURE CLASSIFICATION DATABASES
ALIGNMENT OF PROTEIN STRUCTURES
STRUCTURAL PREDICTION
EVALUATING THE SUCCESS OF STRUCTURE PREDICTIONS
STRUCTURAL MODELING
SUMMARY AND FUTURE PROSPECTS
REFERENCES
Genome Analysis
INTRODUCTION
GENOME ANATOMY
SEQUENCE ASSEMBLY AND GENE IDENTIFICATION
METHODS
COMPARATIVE GENOMICS
FUNCTIONAL CLASSIFICATION OF GENES
GENE ORDER (SYNTENY) IS CONSERVED ON CHROMOSOMES OF RELATED ORGANISMS
GLOBAL GENE REGULATION
PREDICTION OF GENE FUNCTION BASED ON A COMPOSITE ANALYSIS
PUTTING TOGETHER ALL OF THE INFORMATION INTO A GENOME DATABASE
REFERENCES
Glossary
Index