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Sequence - Evolution - Function Computational Approaches in Comparative Genomics

ISBN-10: 1402072740

ISBN-13: 9781402072741

Edition: 2003

Authors: Eugene V. Koonin, Michael Y. Galperin

List price: $215.00
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Description:

This is an introduction to the computational approaches that play a critical role in the emerging branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches to the subject.
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Book details

List price: $215.00
Copyright year: 2003
Publisher: Springer
Publication date: 11/30/2002
Binding: Hardcover
Pages: 462
Size: 6.50" wide x 9.50" long x 1.25" tall
Weight: 2.090
Language: English

Preface
Introduction: Personal Interludes
Genomes from Phage to Human
The humble beginnings
...and the astonishing progress of genome sequencing
Basic questions of comparative genomics
Further reading
The Evolutionary Concept in Genetics and Genomics
Similarity, homology, divergence and convergence
The critical definitions
Conservation of protein sequence and structure in evolution
Homologs: orthologs and paralogs
Patterns and mechanisms in genome evolution
Evolution of gene order
Lineage-specific gene loss
Lineage-specific expansion of gene families
Horizontal (lateral) gene transfer
Non-orthologous gene displacement and the minimal gene set concept
Phyletic patterns (profiles)
Conclusions and outlook
Further reading
Information Sources for Genomics
General purpose sequence databases
Nucleotide sequence databases
Protein sequence databases
Reliability of the database entries
Protein sequence motifs and domain databases
Motif databases
Domain databases
Integrated motif and domain databases
Protein structure databases
Specialized genomics databases
Organism-specific databases
Prokaryotes
Unicellular eukaryotes
Multicellular eukaryotes
Taxonomy, protein interactions, and other databases
Taxonomy databases
Signal transduction and protein interaction databases
Biochemical databases
PubMed
Specifying the terms in PubMed search
Interpretation of the search pattern
NCBI Bookshelf
Conclusions and outlook
Further reading
Principles and Methods of Sequence Analysis
Identification of genes in a genomic DNA sequence
Prediction of protein-coding genes
Algorithms and software tools for gene identification
Principles of sequence similarity searches
Substitution scores and substitution matrices
Statistics of protein sequence comparison
Protein sequence complexity. Compositional bias
Algorithms for sequence alignment and similarity search
The basic alignment concepts and principal algorithms
Sequence database search algorithms
Motifs, domains and profiles
Practical issues: how to get the most out of BLAST
Setting up the BLAST search
Choosing the BLAST parameters
Running BLAST and formatting the output
Analysis and interpretation of BLAST results
The road to discovery
Protein annotation in the absence of detectable homologs
Prediction of subcellular localization of the protein
Prediction of structural features of the protein
Threading
Conclusions and outlook
Further reading
Genome Annotation and Analysis
Methods, approaches and results in genome annotation
Genome annotation: data flow and performance
Automation of genome annotation
Accuracy of genome annotation
A case study on genome annotation
Genome context analysis and functional prediction
Phyletic patterns (profiles)
Gene (domain) fusions: "Rosetta Stone"
Gene clusters and genomic neighborhoods
Conclusions and outlook
Further reading
Comparative Genomics and New Evolutionary Biology
The three domains of life
Prevalence of lineage-specific gene loss and horizontal gene transfer
The Tree of Life: before and after the genomes
Phylogenetic trees in the pre-genomic era
Comparative genomics threatens the species tree concept
Genome trees - can comparative genomics help build a consensus?
The genomic clock
The major transitions in evolution: a comparative-genomic perspective
Ancestral life form and evolutionary reconstructions
Beyond LUCA, back to the RNA world
A brief history of early life
The prokaryote-eukaryote transition and origin of novelty in eukaryotes
Conclusions and outlook: evolution tinkers with fluid genomes
Further Reading
Evolution of Central Metabolic Pathways: The Playground of Non-orthologous Gene Displacement
Carbohydrate metabolism
Glycolysis
Gluconeogenesis
Entner-Doudoroff pathway and pentose phosphate shunt
TCA cycle
Pyrimidine biosynthesis
Purine biosynthesis
Amino acid biosynthesis
Biosynthesis of aromatic amino acids
Arginine biosynthesis
Histidine biosynthesis
Biosynthesis of branched-chain amino acids
Proline biosynthesis
Coenzyme biosynthesis
Thiamin
Riboflavin
NAD
Biotin
Heme
Pyridoxine
Microbial enzymes as drug targets
Potential targets for broad-spectrum drugs
Potential targets for pathogen-specific drugs
Conclusions and outlook
Further reading
Genomes and the Protein Universe
The protein universe is highly structured and there are few common folds
Counting the beans: structural genomics, distributions of protein folds and superfamilies in genomes and some models of genome evolution
Evolutionary dynamics of multidomain proteins
Conclusions and outlook
Further reading
Epilogue: Peering through the crystal ball
Functional genomics: a programme of prediction-driven research?
Digging up genomic junkyards
"Dreams of a final theory"
Appendices
Glossary
Useful WWW sites
Databases
Major genome sequencing centers
Problems
References
Index