Essential Bioinformatics

Preface			page ix
SECTION I INTRODUCTION AND BIOLOGICAL DATABASES
1	Introduction		3
		What Is Bioinformatics?	4
		Goal	5
		Scope	5
		Applications	6
		Limitations	7
		New Themes	8
		Further Reading	8
2	Introduction to Biological Databases		10
		What Is a Database?	10
		Types of Databases	10
		Biological Databases	13
		Pitfalls of Biological Databases	17
		Information Retrieval from Biological Databases	18
		Summary	27
		Further Reading	27
SECTION II SEQUENCE ALIGNMENT
3	Pairwise Sequence Alignment		31
		Evolutionary Basis	31
		Sequence Homology versus Sequence Similarity	32
		Sequence Similarity versus Sequence Identity	33
		Methods	34
		Scoring Matrices	41
		Statistical Significance of Sequence Alignment	47
		Summary	48
		Further Reading	49
4	Database Similarity Searching		51
		Unique Requirements of Database Searching	51
		Heuristic Database Searching	52
		Basic Local Alignment Search Tool (BLAST)	52
		FASTA	57
		Comparison of FASTA and BLAST	60
		Database Searching with the Smith–Waterman Method	61
		Summary	61
		Further Reading	62
5	Multiple Sequence Alignment		63
		Scoring Function	63
		Exhaustive Algorithms	64
		Heuristic Algorithms	65
		Practical Issues	71
		Summary	73
		Further Reading	74
6	Profiles and Hidden Markov Models		75
		Position-Specific Scoring Matrices	75
		Profiles	77
		Markov Model and Hidden Markov Model	79
		Summary	84
		Further Reading	84
7	Protein Motifs and Domain Prediction		85
		Identification of Motifs and Domains in Multiple Sequence Alignment	86
		Motif and Domain Databases Using Regular Expressions	86
		Motif and Domain Databases Using Statistical Models	87
		Protein Family Databases	90
		Motif Discovery in Unaligned Sequences	91
		Sequence Logos	92
		Summary	93
		Further Reading	94
SECTION III GENE AND PROMOTER PREDICTION
8	Gene Prediction		97
		Categories of Gene Prediction Programs	97
		Gene Prediction in Prokaryotes	98
		Gene Prediction in Eukaryotes	103
		Summary	111
		Further Reading	111
9	Promoter and Regulatory Element Prediction		113
		Promoter and Regulatory Elements in Prokaryotes	113
		Promoter and Regulatory Elements in Eukaryotes	114
		Prediction Algorithms	115
		Summary	123
		Further Reading	124
SECTION IV MOLECULAR PHYLOGENETICS
10	Phylogenetics Basics		127
		Molecular Evolution and Molecular Phylogenetics	127
		Terminology	128
		Gene Phylogeny versus Species Phylogeny	130
		Forms of Tree Representation	131
		Why Finding a True Tree Is Difficult	132
		Procedure	133
		Summary	140
		Further Reading	141
11	Phylogenetic Tree Construction Methods and Programs		142
		Distance-Based Methods	142
		Character-Based Methods	150
		Phylogenetic Tree Evaluation	163
		Phylogenetic Programs	167
		Summary	168
		Further Reading	169
SECTION V STRUCTURAL BIOINFORMATICS
12	Protein Structure Basics		173
		Amino Acids	173
		Peptide Formation	174
		Dihedral Angles	175
		Hierarchy	176
		Secondary Structures	178
		Tertiary Structures	180
		Determination of Protein Three-Dimensional Structure	181
		Protein Structure Database	182
		Summary	185
		Further Reading	186
13	Protein Structure Visualization, Comparison, and Classification		187
		Protein Structural Visualization	187
		Protein Structure Comparison	190
		Protein Structure Classification	195
		Summary	199
		Further Reading	199
14	Protein Secondary Structure Prediction		200
		Secondary Structure Prediction for Globular Proteins	201
		Secondary Structure Prediction for Transmembrane Proteins	208
		Coiled Coil Prediction	211
		Summary	212
		Further Reading	213
15	Protein Tertiary Structure Prediction		214
		Methods	215
		Homology Modeling	215
		Threading and Fold Recognition	223
		Ab Initio Protein Structural Prediction	227
		CASP	228
		Summary	229
		Further Reading	230
16	RNA Structure Prediction		231
		Introduction	231
		Types of RNA Structures	233
		RNA Secondary Structure Prediction Methods	234
		Ab Initio Approach	234
		Comparative Approach	237
		Performance Evaluation	239
		Summary	239
		Further Reading	240
SECTION VI GENOMICS AND PROTEOMICS
17	Genome Mapping, Assembly, and Comparison		243
		Genome Mapping	243
		Genome Sequencing	245
		Genome Sequence Assembly	246
		Genome Annotation	250
		Comparative Genomics	255
		Summary	259
		Further Reading	259
18	Functional Genomics		261
		Sequence-Based Approaches	261
		Microarray-Based Approaches	267
		Comparison of SAGE and DNA Microarrays	278
		Summary	279
		Further Reading	280
19	Proteomics		281
		Technology of Protein Expression Analysis	281
		Posttranslational Modification	287
		Protein Sorting	289
		Protein–Protein Interactions	291
		Summary	296
		Further Reading	296
APPENDIX
Appendix 1. Practical Exercises			301
Appendix 2. Glossary			318
Index			331

Resources and solutions

Details

Jin Xiong

Texas A & M University

Paperback

For price and ordering options, inspection copy requests, and reading lists please select:

Contents

Quick search

Related areas