Sequence - Evolution - Function

by Koonin, Eugene V.; Galperin, Michael Y.

• ISBN13: 9781402072741
• ISBN10: 1402072740
• Format: Hardcover
• Copyright: 2002-12-01
• Publisher: Kluwer Academic Pub

Summary

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Key topics covered in this textbook are: *the completed and ongoing genome sequencing projects, *databases that store and organize genomic data, with their unique advantages and pitfalls, *principles and methods of genome analysis and annotation, *ways to automate the searches and increase search sensitivity while minimizing the error rate, *the first lessons from the Human Genome Project, *the contribution of comparative genomics to the understanding of hereditary diseases and cancer, *fundamental and practical applications of comparative genomics, *the use of complete genomes for evolutionary analysis, *the application of comparative genomics for identification of potential drug targets in microbial genomes, *Problems for Further Study, which are designed to be solved by using methods available through the WWW. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Author Biography

Eugene V. Koonin is a Senior Investigator and Michael Y. Galperin is a Staff Scientist at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland

Table of Contents

Preface	ix
Introduction. Personal Interludes	1	(2)
Genomes from Phage to Human	3	(22)
The humble beginnings	3	(10)
...and the astonishing progress of genome sequencing	13	(5)
Basic questions of comparative genomics	18	(6)
Further reading	24	(1)
The Evolutionary Concept in Genetics and Genomics	25	(26)
Similarity, homology, divergence and convergence	25	(12)
The critical definitions	25	(5)
Conservation of protein sequence and structure in evolution	30	(4)
Homologs: orthologs and paralogs	34	(3)
Patterns and mechanisms in genome evolution	37	(12)
Evolution of gene order	37	(1)
Lineage-specific gene loss	38	(2)
Lineage-specific expansion of gene families	40	(2)
Horizontal (lateral) gene transfer	42	(1)
Non-orthologous gene displacement and the minimal gene set concept	43	(4)
Phyletic patterns (profiles)	47	(2)
Conclusions and outlook	49	(1)
Further reading	49	(2)
Information Sources for Genomics	51	(60)
General purpose sequence databases	51	(13)
Nucleotide sequence databases	51	(1)
Protein sequence databases	52	(5)
Reliability of the database entries	57	(7)
Protein sequence motifs and domain databases	64	(11)
Motif databases	64	(5)
Domain databases	69	(4)
Integrated motif and domain databases	73	(2)
Protein structure databases	75	(6)
Specialized genomics databases	81	(8)
Organism-specific databases	89	(9)
Prokaryotes	89	(3)
Unicellular eukaryotes	92	(1)
Multicellular eukaryotes	93	(5)
Taxonomy, protein interactions, and other databases	98	(6)
Taxonomy databases	98	(1)
Signal transduction and protein interaction databases	99	(2)
Biochemical databases	101	(3)
PubMed	104	(5)
Specifying the terms in PubMed search	104	(3)
Interpretation of the search pattern	107	(2)
NCBI Bookshelf	109	(1)
Conclusions and outlook	109	(1)
Further reading	110	(1)
Principles and Methods of Sequence Analysis	111	(82)
Identification of genes in a genomic DNA sequence	112	(14)
Prediction of protein-coding genes	112	(6)
Algorithms and software tools for gene identification	118	(8)
Principles of sequence similarity searches	126	(14)
Substitution scores and substitution matrices	127	(6)
Statistics of protein sequence comparison	133	(3)
Protein sequence complexity. Compositional bias	136	(4)
Algorithms for sequence alignment and similarity search	140	(19)
The basic alignment concepts and principal algorithms	140	(5)
Sequence database search algorithms	145	(3)
Motifs, domains and profiles	148	(11)
Practical issues: how to get the most out of BLAST	159	(13)
Setting up the BLAST search	159	(1)
Choosing the BLAST parameters	160	(4)
Running BLAST and formatting the output	164	(2)
Analysis and interpretation of BLAST results	166	(6)
The road to discovery	172	(9)
Protein annotation in the absence of detectable homologs	181	(11)
Prediction of subcellular localization of the protein	181	(3)
Prediction of structural features of the protein	184	(4)
Threading	188	(4)
Conclusions and outlook	192	(1)
Further reading	192	(1)
Genome Annotation and Analysis	193	(34)
Methods, approaches and results in genome annotation	193	(17)
Genome annotation: data flow and performance	193	(4)
Automation of genome annotation	197	(2)
Accuracy of genome annotation	199	(7)
A case study on genome annotation	206	(4)
Genome context analysis and functional prediction	210	(15)
Phyletic patterns (profiles)	210	(4)
Gene (domain) fusions: ``Rosetta Stone''	214	(4)
Gene clusters and genomic neighborhoods	218	(7)
Conclusions and outlook	225	(1)
Further reading	226	(1)
Comparative Genomics and New Evolutionary Biology	227	(68)
The three domains of life	228	(5)
Prevalence of lineage-specific gene loss and horizontal gene transfer	233	(10)
The Tree of Life: before and after the genomes	243	(9)
Phylogenetic trees in the pre-genomic era	243	(1)
Comparative genomics threatens the species tree concept	244	(1)
Genome trees - can comparative genomics help build a consensus?	245	(6)
The genomic clock	251	(1)
The major transitions in evolution: a comparative-genomic perspective	252	(40)
Ancestral life form and evolutionary reconstructions	252	(12)
Beyond LUCA, back to the RNA world	264	(4)
A brief history of early life	268	(3)
The prokaryote-eukaryote transition and origin of novelty in eukaryotes	271	(21)
Conclusions and outlook: evolution tinkers with fluid genomes	292	(2)
Further Reading	294	(1)
Evolution of Central Metabolic Pathways: The Playground of Non-orthologous Gene Displacement	295	(62)
Carbohydrate metabolism	296	(20)
Glycolysis	296	(7)
Gluconeogenesis	303	(3)
Entner-Doudoroff pathway and pentose phosphate shunt	306	(5)
TCA cycle	311	(5)
Pyrimidine biosynthesis	316	(4)
Purine biosynthesis	320	(6)
Amino acid biosynthesis	326	(16)
Biosynthesis of aromatic amino acids	326	(8)
Arginine biosynthesis	334	(3)
Histidine biosynthesis	337	(2)
Biosynthesis of branched-chain amino acids	339	(1)
Proline biosynthesis	340	(2)
Coenzyme biosynthesis	342	(7)
Thiamin	342	(1)
Riboflavin	343	(1)
NAD	344	(1)
Biotin	345	(1)
Heme	346	(2)
Pyridoxine	348	(1)
Microbial enzymes as drug targets	349	(5)
Potential targets for broad-spectrum drugs	351	(1)
Potential targets for pathogen-specific drugs	352	(2)
Conclusions and outlook	354	(1)
Further reading	355	(2)
Genomes and the Protein Universe	357	(14)
The protein universe is highly structured and there are few common folds	357	(4)
Counting the beans: structural genomics, distributions of protein folds and superfamilies in genomes and some models of genome evolution	361	(5)
Evolutionary dynamics of multidomain proteins	366	(3)
Conclusions and outlook	369	(1)
Further reading	369	(2)
Epilogue: Peering through the crystal ball	371	(10)
Functional genomics: a programme of prediction-driven research?	371	(5)
Digging up genomic junkyards	376	(3)
``Dreams of a final theory''	379	(2)
Appendices	381	(22)
1. Glossary	381	(8)
2. Useful WWW sites	389	(6)
Databases	389	(3)
Major genome sequencing centers	392	(3)
3. Problems	395	(8)
References	403	(54)
Index	457