Sequence — Evolution — Function: Computational Approaches in Comparative GenomicsSpringer 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: |
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 |
455 | |
Otras ediciones - Ver todas
Sequence — Evolution — Function: Computational Approaches in Comparative ... Eugene V. Koonin,Michael Galperin Vista previa limitada - 2013 |
Sequence — Evolution — Function: Computational Approaches in Comparative ... Eugene Koonin,Michael Y. Galperin Sin vista previa disponible - 2010 |
Sequence — Evolution — Function: Computational Approaches in Comparative ... Eugene Koonin,Michael Y. Galperin Sin vista previa disponible - 2013 |