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Tables of Contents for Sequence - Evolution - Function
Chapter/Section Title
Page #
Page Count
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