Sequence — Evolution — Function: Computational Approaches in Comparative Genomics

Portada
Springer Science & Business Media, 2002 M11 30 - 462 páginas

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.

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I am constantly referring this book to people to read, since even though it was published nearly a decade ago, it contains the very basic underpinnings of the field of comparative/functional genomics, by two scientists whose work was very influential in creating that field. Perhaps what impressed me most (and the reason I keep referring it to others) was that it contains the most accessible description of sequence homology searches that I have ever read, giving practical advice on how to get the most out of BLAST and related homology search tools. In fact, I was so impressed by this book and the work done in Koonin's group at NCBI that I even joined his lab to learn more (and therefore my review should be considered biased, although since I read it first before joining, perhaps not completely so). 

Contenido

FROM PHAGE TO HUMAN
3
12 and the Astonishing Progress of Genome Sequencing
13
13 Basic Questions of Comparative Genomics
18
14 Further Reading
24
CHAPTER 2 EVOLUTIONARY CONCEPT IN GENETICS AND GENOMICS
25
212 Conservation of protein sequence and structure in evolution
30
orthologs and paralogs
34
22 Patterns and Mechanisms in Genome Evolution
37
52 Genome Context Analysis and Functional Prediction
210
guilt by association
214
523 Gene clusters and genomic neighborhoods
218
53 Conclusions and Outlook
223
54 Further Reading
224
CHAPTER 6 COMPARATIVE GENOMICS AND NEW EVOLUTIONARY BIOLOGY
225
61 The Three Domains of Life
226
62 Prevalence of LineageSpecific Gene Loss and Horizontal Gene Transfer in Evolution
231

222 Lineagespecific gene loss
38
223 Lineagespecific expansion of gene families
40
224 Horizontal lateral gene transfer
42
225 Nonorthologous gene displacement and the minimal gene set concept
43
226 Phyletic patterns profiles
47
23 Conclusions and outlook
49
CHAPTER 3 INFORMATION SOURCES FOR GENOMICS
51
312 Protein sequence databases
52
313 Reliability of database entries
57
32 Protein Sequence Motifs and Domain Databases
64
322 Domain databases
69
323 Integrated motif and domain databases
73
33 Protein Structure Databases
75
34 Specialized Genomics Databases
81
35 Organismspecific Databases
89
352 Unicellular eukaryotes
92
353 Multicellular eukaryotes
93
36 Taxonomy Protein Interactions and Other Databases
98
362 Signal transduction regulation proteinprotein interaction and other useful databases
99
363 Biochemical databases
101
37 PubMed
104
372 Interpretation of the search pattern
107
373 NCBI Bookshelf
109
39 Further Reading
110
CHAPTER 4 PRINCIPLES AND METHODS OF SEQUENCE ANALYSIS
111
41 Identification of Genes in a Genomic DNA Sequence
112
412 Algorithms and software tools for gene identification
118
42 Principles of Sequence Similarity Searches
126
421 Substitution scores and substitution matrices
127
422 Statistics of protein sequence comparison
133
423 Protein sequence complexity Compositional bias
136
43 Algorithms for Sequence Alignment and Similarity Search
140
432 Sequence database search algorithms
145
433 Motifs domains and profiles
148
How to Get the Most out of BLAST
159
442 Choosing BLAST parameters
160
443 Running BLAST and formatting the output
164
separating wheat from the chaff
166
45 The Road to Discovery
172
46 Protein Annotation in the Absence of Detectable Homologs
181
462 Prediction of structural features of proteins
184
463 Threading
188
47 Conclusions and Outlook
192
CHAPTER 5 GENOME ANNOTATION AND ANALYSIS
193
512 Automation of genome annotation
197
513 Accuracy of genome annotation sources of errors and some thoughts on possible improvements
199
the crenarchaeon Aeropyrum pernix
206
Before and After the Genome
241
632 Comparative genomics threatens the species tree concept
242
633 Genometrees can comparative genomics help build a consensus?
243
634 The genomic clock
249
A Comparative Genomic Perspective
250
642 Beyond LUCA back to the RNA world
262
643 A brief history of early life
266
644 The prokaryoteeukaryote transition and origin of novelty in eukaryotes
269
Evolution Tinkers with Fluid Genomes
290
66 Further Reading
292
THE PLAYGROUND OF NONORTHOLOGOUS GENE DISPLACEMENT
293
71 Carbohydrate Metabolism
294
712 Gluconeogenesis
301
713 EntnerDoudoroff pathway and pentose phosphate shunt
304
714 The TCA cycle
309
72 Pyrimidine Biosynthesis
314
73 Purine Biosynthesis
318
74 Amino Acid Biosynthesis
324
742 Arginine biosynthesis
332
743 Histidine biosynthesis
335
744 Biosynthesis of branchedchain amino acids
337
745 Proline biosynthesis
338
75 Coenzyme Biosynthesis
340
752 Riboflavin
341
753 NAD
342
754 Biotin
343
755 Heme
344
756 Pyridoxine
346
76 Microbial Enzymes as Potential Drug Targets
347
761 Potential targets for broadspectrum drugs
349
762 Potential targets for pathogenspecific drugs
350
77 Conclusions and Outlook
352
78 Further Reading
353
CHAPTER 8 GENOMES AND THE PROTEIN UNIVERSE
355
Structural Genomics Distributions of Protein Folds and Superfamilies in Genomes and Some Models of Genome Evolution
359
83 Evolutionary Dynamics of Multidomain Proteins and Domain Accretion
364
84 Conclusions and Outlook
367
PEERING THROUGH THE CRYSTAL BALL
369
92 Digging up Genomic Junkyards
374
93 Dreams of a final theory
377
APPENDICES
379
2 Useful Web Sites
387
22 Major genome sequencing centers
390
3 Problems
393
References
401
INDEX
455
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