Handbook of comparative genomics: principles and methodology
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| Main Authors: | , |
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| Format: | Book |
| Language: | English |
| Published: |
New York
Wiley-Liss
2003
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| Subjects: | |
| Online Access: | Publisher description Table of contents Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references (p. 377-422) and index |
| Physical Description: | XIV, 427 S. graph. Darst. |
| ISBN: | 047139128X |
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Record in the Search Index
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| adam_text | HANDBOOK OF
COMPARATIVE GENOMICS
Principles and Methodology
CECILIASACCONE
Department of Biochemistry and Molecular Biology
University of Bari
Italy
GRAZIANO PESOLE
Department of Physiology and General Biochemistry
University of Milan
Italy
WILEY-LISS
A JOHN WILEY amp; SONS PUBLICATION
CONTENTS
PREFACE xiii
I GENOME FEATURES 1
1 PROKARYOTES 3
1 1 Introduction / 3
1 2 Morphology and Classification / 8
1 3 Genome Shape and Size / 10
1 4 Gene Content and Organization / 16
1 5 Base Composition / 20
1 6 Codon Use h21
1 7 Replication and Expression / 29
2 1 Introduction / 36
2 2 Classification and Time Scale / 36
2 3 Genome Shape and Size / 40
2 4 Base Composition / 46
2 5 Replication, Repair, and Recombination / 48
2 6 Gene Expression / 53
261 Transcription and Posttranscriptional Regulation / 53
262 Genetic Code and Codon Use / 59
263 Translation and Posttranslation Modifications / 61
2 EUKARYOTES 36
vii
Viii CONTENTS
2 7 Completely Sequenced Eukaryotic Genomes / 64
271 Saccharomyces cerevisiae Genome / 66
272 Schizosaccharomyces pombe Genome / 69
273 Caenorhabditis elegans Genome / 70
274 Drosophila melanogaster Genome / 72
275 Arabidopsis thaliana Genome / 74
276 Oryza sativa Genome / 77
277 Homo sapiens Genome / 78
3 ORGANELLES 85
3 1 Mitochondria / 85
311 General Structure and Function / 85
312 DNA and Genetic System / 88
313 Genome Features / 97
3 2 Chloroplasts and Other Plastids / 125
II METHODOLOGIES 131
4 MOLECULAR BIOLOGY TECHNIQUES FOR GENOMICS 133
4 1 Genome DNA Sequencing / 133
411 DNA-Sequencing Techniques / 133
412 The Human Genome Project / 136
4 2 Analysis of the Transcriptome / 137
421 Analysis of Gene Expression / 137
422 Expressed Sequence Tags / 138
423 Serial Analysis of Gene Expression / 139
424 Differential Display / 141
425 Representional Difference Analysis / 142
426 DNA Microarrays / 143
4 3 Analysis of the Proteome / 149
431 Two-Dimensional Gel Electrophoresis / 151
432 Protein Identification / 151
433 Study of Protein-DNA and Protein-Protein Interactions / 155
434 Proteome Analysis Using Biochips / 157
5 BIOLOGICAL DATABASES IN THE GENOMIC ERA 159
5 1 Introduction / 159
5 2 Primary and Specialized Databases / 159
5 3 Database Structures / 162
5 4 Linked Databases and Database Interoperability / 163
CONTENTS
5 5 Database Annotation / 166
5 6 Retrieval Systems / 169
561 SRS / 169
562 Entrez / 169
563 Other Retrieval Systems / 170
5 7 Nucleotide Databases / 170
5 8 Protein Databases / 171
5 9 Other Protein Databases / 171
5 10 Genomic Databases and Resources / 174
5 11 Gene Databases and Resources / 179
5 12 Transcriptome Databases / 180
5 13 Metabolism Databases / 181
5 14 Mutation Databases / 182
5 15 Mitochondrial Databases and Resources / 184
6 COMPUTATIONAL METHODS FOR THE ANALYSIS OF
GENOME SEQUENCE DATA
6 1 Introduction / 187
6 2 Dot-Plot Matrix / 188
6 3 Sequence Pairwise Alignment / 189
631 Needleman-Wunsch Global Alignment Algorithm / 191
632 Smith-Waterman Algorithm for the Identification of
Common Molecular Subsequences / 193
633 Alignment of cDNA and Genomic DNA Sequences / 196
634 Genome Alignment / 198
635 Cleanup of Sequence Databases from Redundancy / 201
636 Measure of the Similarity Degree between Homologous
Sequences / 203
6 4 Database Searching / 208
641 FASTA / 209
642 BLAST / 211
643 BLAST and FASTA Family of Programs / 215
644 Filtering Matches to Unwanted Sequences / 216
645 Filtering Matches to Repetitive Sequences / 221
646 Statistical Significance of Alignment Scores / 223
6 5 Multiple Alignment / 226
6 6 Alignment Profiles to Recognize Distantly Related Protein or
Protein Modules / 230
6 7 Methods for Sequence Assembly / 234
671 Sequence Cleaning / 236
672 Sequence Clustering / 237
673 Construction of Alignment Consensus / 238
X CONTENTS
674 Sequence Mapping by Electronic PCR / 240
675 Sequence Assembly in Genome and EST Projects / 240
676 Sequence Assembly for Gene Index Construction / 243
6 8 Linguistic Analysis of Biosequences / 245
681 Biosequences as Markov Chains / 248
682 Linguistic Complexity of Biosequences / 249
683 Identification of Repeats in Genomic Sequences / 253
684 Pattern Searching in Biosequences / 254
685 Identification of Promoter Regions in Chromosomal
Sequences / 261
686 Pattern Discovery for the Identification of Gene Regulatory
Elements and of Protein Motif Models / 262
687 Gene Prediction / 265
688 Identification of CpG Islands in Genomic Sequences / 269
689 Analysis of Codon Use Strategy / 271
6 9 Prediction of RNA Secondary Structures / 273
6 10 Protein Sequence Analysis / 280
6 10 1 Analysis of Protein Primary Sequences / 281
6 10 2 Prediction of Transmembrane Protein Helices / 285
6 10 3 Identification of Protein Signal Peptides and Prediction of Their
Subcellular Location / 290
6 10 4 Prediction of Protein Secondary Structure / 293
6 10 5 Prediction of Coiled-Coil and Helix-Turn-Helix Structures / 298
6 10 6 Prediction of Protein Tertiary Structure / 300
6 10 7 Protein Fold Recognition and Classification / 302
6 10 8 Comparative Evolutionary Genomic Tools for Predicting
Protein Function / 303
6 11 Evolutionary and Phylogenetic Analysis / 306
6 11 1 Estimating Genetic Distances between Homologous
Sequences / 306
6 11 2 Molecular Phylogeny / 309
III COMPARATIVE GENOMICS 325
7 MOLECULAR EVOLUTION 327
7 1 Introduction / 327
7 2 Evolution of Genome Size / 328
7 3 Role of Base Composition in Evolution / 332
7 4 Evolution of the Prokaryotic Genome / 337
7 5 From Prokaryotes to Eukaryotes / 338
751 Origin of the Eukaryotic Cell / 338
CONTENTS Xi
752 Evolution of the Mitochondrial Genome I 340
753 Origin and Evolution of Plastids / 346
7 6 From Unicellular to Multicellular State / 349
7 7 Evolution of the Nuclear Genome / 351
771 Introns / 351
772 Gene and Protein Number / 352
773 Noncoding Elements / 353
774 Expansion of Gene Families / 353
775 Genome Duplication / 360
776 Conclusion / 361
8 MOLECULAR PHYLOGENY 362
8 1 Introduction / 362
8 2 Molecular Clock / 363
8 3 Similarity Measure: Orthology Versus Paralogy I 364
8 4 Molecular Phylogeny in the Genomics Era / 367
8 5 Interrelationships between Distant Taxa: The Tree of Life / 369
8 6 Phylogeny of Metazoans / 370
861 Organellar versus Nuclear Taxonomy / 370
862 Phylogeny of Mammals / 371
APPENDIX: URLs Cited in the Text 375
REFERENCES 377
INDEX 423
|
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| spelling | Saccone, Cecilia Verfasser aut Handbook of comparative genomics principles and methodology Cecilia Saccone, Graziano Pesole New York Wiley-Liss 2003 XIV, 427 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references (p. 377-422) and index Génomique - Guides, manuels, etc Génétique évolutive - Guides, manuels, etc Computational Biology Evolution, Molecular Evolutionary genetics Handbooks, manuals, etc Genomics Genomics Handbooks, manuals, etc Sequence Analysis, DNA Genanalyse (DE-588)4200230-8 gnd rswk-swf Genanalyse (DE-588)4200230-8 s DE-604 Pesole, Graziano Verfasser aut http://www.loc.gov/catdir/description/wiley035/2002011158.html Publisher description http://www.loc.gov/catdir/toc/wiley031/2002011158.html Table of contents HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009920417&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Saccone, Cecilia Pesole, Graziano Handbook of comparative genomics principles and methodology Génomique - Guides, manuels, etc Génétique évolutive - Guides, manuels, etc Computational Biology Evolution, Molecular Evolutionary genetics Handbooks, manuals, etc Genomics Genomics Handbooks, manuals, etc Sequence Analysis, DNA Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4200230-8 |
| title | Handbook of comparative genomics principles and methodology |
| title_auth | Handbook of comparative genomics principles and methodology |
| title_exact_search | Handbook of comparative genomics principles and methodology |
| title_full | Handbook of comparative genomics principles and methodology Cecilia Saccone, Graziano Pesole |
| title_fullStr | Handbook of comparative genomics principles and methodology Cecilia Saccone, Graziano Pesole |
| title_full_unstemmed | Handbook of comparative genomics principles and methodology Cecilia Saccone, Graziano Pesole |
| title_short | Handbook of comparative genomics |
| title_sort | handbook of comparative genomics principles and methodology |
| title_sub | principles and methodology |
| topic | Génomique - Guides, manuels, etc Génétique évolutive - Guides, manuels, etc Computational Biology Evolution, Molecular Evolutionary genetics Handbooks, manuals, etc Genomics Genomics Handbooks, manuals, etc Sequence Analysis, DNA Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Génomique - Guides, manuels, etc Génétique évolutive - Guides, manuels, etc Computational Biology Evolution, Molecular Evolutionary genetics Handbooks, manuals, etc Genomics Genomics Handbooks, manuals, etc Sequence Analysis, DNA Genanalyse |
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