Bioinformatics and functional genomics:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Hoboken, N.J.
Wiley-Blackwell
2009
|
| Ausgabe: | 2. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXVIII, 951 S. Ill., graph. Darst. |
| ISBN: | 9780470085851 |
Internformat
MARC
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| 100 | 1 | |a Pevsner, Jonathan |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Bioinformatics and functional genomics |c Jonathan Pevsner |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a Hoboken, N.J. |b Wiley-Blackwell |c 2009 | |
| 300 | |a XXVIII, 951 S. |b Ill., graph. Darst. | ||
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| 650 | 7 | |a Bioinformática |2 larpcal | |
| 650 | 7 | |a Genomas (processamento de dados) |2 larpcal | |
| 650 | 4 | |a Genomics | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Proteomics | |
| 650 | 4 | |a Computational Biology |x methods | |
| 650 | 4 | |a Genetic Techniques | |
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Datensatz im Suchindex
| _version_ | 1804138325854912512 |
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| adam_text | Titel: Bioinformatics and functional genomics
Autor: Pevsner, Jonathan
Jahr: 2009
intents in Brie:
part i mm m. m m ran sequences in darbases
I Introduction, 3
Access to Sequence Data and Literature Information, 13
J Pairwise Sequence Alignment, 47
i Basic Local Alignment Search Tool (BLAST), 101
3 Advanced Database Searching, 141
n
D Multiple Sequence Alignment, 1 79
/ Molecular Phylogeny and Evolution, 215
PART II GlIiEfMSIFllPIBN
o
0 Bioinformatic Approaches to Ribonucleic Acid (RNA), 279
a Gene Expression: Microarray Data Analysis, 331
lu Protein Analysis and Proteomics, 379
II Protein Structure, 421
I/ Functional Genomics, 461
PART III GENOME ANALYSIS
IJ Completed Genomes, 517
n Completed Genomes: Viruses, 567
3 Completed Genomes: Bacteria and Archaea, 597
in
ID The Eukaryotic Chromosome, 639
1/ Eukaryotic Genomes: Fungi, 697
in
10 Eukaryotic Genomes: From Parasites to Primates, 729
lo Human Genome, 791
90
ill Human Disease, 839
Glossary, 891
Answers to Self-Test Quizzes, 909
Author Index, 911
Subject Index, 913
vii
intents
Preface to the Second Edition, xxi
Preface to the First Edition, xxiii
Foreword, xxvii
PARTI KDU1DHHKES
IN IKES
I Introduction, 3
Organization of The Book, 4
Bioinformatics: The Big Picture, 4
A Consistent Example:
Hemoglobin, 8
Organization of The Chapters, 9
A Textbook for Courses on
Bioinformatics and
Genomics, 9
Key Bioinformatics Websites, 10
Suggested Reading, 11
References, 11
/ Access to Sequence Data and
Literature Information, 13
Introduction to Biological
Databases, 13
GenBank: Database of Most Known
Nucleotide and Protein
Sequences, 14
Amount of Sequence Data, 15
Organisms in GenBank, 16
Types of Data in GenBank, 18
Genomic DNA Databases, 19
cDNA Databases Corresponding
to Expressed Genes, 19
Expressed Sequence Tags
(ESTs), 19
ESTs and UniGene, 20
Sequence-Tagged Sites
(STSs), 22
Genome Survey Sequences
(GSSs), 22
High Throughput Genomic
Sequence (HTGS), 23
Protein Databases, 23
National Center for Biotechnology
Information, 23
Introduction to NCBI: Home
Page, 23
PubMed, 23
Entrez, 24
BLAST, 25
OMIM, 25
Books, 25
Taxonomy, 25
Structure, 25
The European Bioinformatics
Institute (EBI), 25
Access to Information: Accession
Numbers to Label and Identify
Sequences, 26
The Reference Sequence (RefSeq)
Project, 27
The Consensus Coding Sequence
(CCDS) Project, 29
Access to Information via Entrez Gene
at NCBI, 29
Relationship of Entrez Gene,
Entrez Nucleotide, and Entrez
Protein, 32
Comparison of Entrez Gene and
UniGene, 32
Entrez Gene and HomoloGene, 33
Access to Information: Protein
Databases, 33
UniProt, 33
The Sequence Retrieval System at
ExPASy, 34
Access to Information: The Three
Main Genome Browsers, 35
The Map Viewer at NCBI, 35
ix
The University of California, Santa
Cruz (UCSC) Genome
Browser, 35
The Ensembl Genome Browser, 35
Examples of How to Access Sequence
Data, 36
HIV pol, 36
Histones, 38
Access to Biomedical Literature, 38
PubMed Central and Movement
toward Free Journal Access, 39
Example of PubMed Search:
RBP, 40
Perspective, 42
Pitfalls, 42
Web Resources, 42
Discussion Questions, 42
Problems, 42
Self-Test Quiz, 43
Suggested Reading, 44
References, 44
n
j Pairwise Sequence Alignment, 47
Introduction, 47
Protein Alignment: Often More
Informative Than DNA
Alignment, 47
Definitions: Homology, Similarity,
Identity, 48
Gaps, 55
Pairwise Alignment, Homology, and
Evolution of Life, 55
Scoring Matrices, 57
Dayhoff Model: Accepted Point
Mutations, 58
PAM1 Matrix, 63
PAM250 and Other PAM
Matrices, 65
From a Mutation Probability Matrix
to a Log-Odds Scoring
Matrix, 69
Practical Usefulness of PAM
Matrices in Pairwise
Alignment, 70
Important Alternative to PAM:
BLOSUM Scoring Matrices, 70
Pairwise Alignment and Limits of
Detection: The Twilight
Zone , 74
Alignment Algorithms: Global and
Local, 75
Global Sequence Alignment:
Algorithm of Needleman and
Wunsch, 76
Step 1: Setting Up a Matrix, 76
Step 2: Scoring the Matrix, 77
Step 3: Identifying the Optimal
Alignment, 79
Local Sequence Alignment: Smith
and Waterman Algorithm, 82
Rapid, Heuristic Versions of
Smith-Waterman: FASTA and
BLAST, 84
Pairwise Alignment with Dot
Plots, 85
The Statistical Significance of Pairwise
Alignments, 86
Statistical Significance of Global
Alignments, 87
Statistical Significance of Local
Alignments, 89
Percent Identity and Relative
Entropy, 90
Perspective, 91
Pitfalls, 94
Web Resources, 94
Discussion Questions, 94
Problems/Computer Lab, 95
Self-Test Quiz, 95
Suggested Reading, 96
References, 97
4 Basic Local Alignment Search
Tool (BLAST), 101
Introduction, 101
BLAST Search Steps, 103
Step 1: Specifying Sequence of
Interest, 103
Step 2: Selecting BLAST
Program, 104
Step 3: Selecting a
Database, 106
Step 4a: Selecting Optional Search
Parameters, 106
1. Query, 107
2. Limit by Entrez Query, 107
3. Short Queries, 107
4. Expect Threshold, 107
5. Word Size, 108
6. Matrix, 110
7. Gap Penalties, 110
8. Composition-Based
Statistics, 110
9. Filtering and Masking, 111
Step 4b: Selecting Formatting
Parameters, 112
BLAST Algorithm Uses Local
Alignment Search Strategy, 115
BLAST Algorithm Parts: List, Scan,
Extend, 115
BLAST Algorithm: Local Alignment
Search Statistics and
E Value, 118
Making Sense of Raw Scores with
Bit Scores, 121
BLAST Algorithm: Relation between
E and p Values, 121
Parameters of a
BLAST Search, 123
BLAST Search Strategies, 123
General Concepts, 123
Principles of BLAST
Searching, 123
How to Evaluate Significance of
Your Results, 1 23
How to Handle Too Many
Results, 128
How to Handle Too Few
Results, 128
BLAST Searching With
Multidomain Protein: HIV-1
pol, 129
Perspective, 134
Pitfalls, 134
Web Resources, 135
Discussion Questions, 135
Computer Lab/Problems, 135
Self-Test Quiz, 136
Suggested Reading, 137
References, 137
u Advanced Database
Searching, 141
Introduction, 141
Specialized BLAST Sites, 142
Organism-Specific BLAST
Sites, 142
Ensembl BLAST, 142
Wellcome Trust Sanger
Institute, 143
Specialized BLAST-Related
Algorithms, 143
WU BLAST 2.0, 144
European Bioinformatics Institute
(EBI), 144
Specialized NCBI BLAST
Sites, 144
Finding Distantly Related Proteins:
Position-Specific Iterated BLAST
(PSI-BLAST), 145
Assessing Performance of
PSI-BLAST, 150
PSI-BLAST Errors: The Problem of
Corruption, 152
Reverse Position-Specific
BLAST, 152
Pattern-Hit Initiated BLAST
(PHI-BLAST), 153
Profile Searches: Hidden Markov
Models, 155
BLAST-Like Alignment Tools to
Search Genomic DNA
Rapidly, 161
Benchmarking to Assess Genomic
Alignment Performance, 162
PatternHunter, 162
BLASTZ, 163
MegaBLAST and Discontiguous
MegaBLAST, 164
BLAT, 166
LAGAN, 168
SSAHA, 168
SIM4, 169
Using BLAST for Gene
Discovery, 169
Perspective, 173
Pitfalls, 173
Web Resources, 174
Discussion Questions, 174
Problems/Computer Lab, 174
Self-Test Quiz, 175
Suggested Reading, 176
References, 176
n
D Multiple Sequence Alignment, 179
Introduction, 179
Definition of Multiple Sequence
Alignment, 180
Typical Uses and Practical Strategies
of Multiple Sequence
Alignment, 181
Benchmarking: Assessment of
Multiple Sequence Alignment
Algorithms, 182
Five Main Approaches to Multiple
Sequence Alignment, 184
Exact Approaches to Multiple
Sequence Alignment, 184
Progressive Sequence
Alignment, 185
Iterative Approaches, 190
Consistency-Based
Approaches, 192
Structure-Based Methods, 194
Conclusions from Benchmarking
Studies, 196
Databases of Multiple Sequence
Alignments, 197
Pfam: Protein Family Database of
Profile HMMs, 197
Smart, 199
Conserved Domain Database, 199
Prints, 201
Integrated Multiple Sequence
Alignment Resources: InterPro
and iProClass, 201
PopSet, 202
Multiple Sequence Alignment
Database Curation: Manual
versus Automated, 202
Multiple Sequence Alignments of
Genomic Regions, 203
Perspective, 206
Pitfalls, 207
Web Resources, 207
Discussion Questions, 207
Problems/Computer Lab, 208
Self-Test Quiz, 208
Suggested Reading, 209
References, 210
/ Molecular Phylogeny and
Evolution, 215
Introduction to Molecular
Evolution, 215
Goals of Molecular
Phylogeny, 216
Historical Background, 217
Molecular Clock
Hypothesis, 221
Positive and Negative
Selection, 227
Neutral Theory of Molecular
Evolution, 230
Molecular Phylogeny: Properties of
Trees, 231
Tree Roots, 233
Enumerating Trees and
Selecting Search
Strategies, 234
Type of Trees, 238
Species Trees versus Gene/Protein
Trees, 238
DNA, RNA, or Protein-Based
Trees, 240
Five Stages of Phylogenetic
Analysis, 243
Stage 1: Sequence
Acquisition, 243
Stage 2: Multiple Sequence
Alignment, 244
Stage 3: Models of DNA
and Amino Acid
Substitution, 246
Stage 4: Tree-Building
Methods, 254
Phylogenetic Methods, 255
Distance, 255
The UPGMA Distance-Based
Method, 256
Making Trees by Distance-
Based Methods: Neighbor
Joining, 259
Phylogenetic Inference: Maximum
Parsimony, 260
Model-Based Phylogenetic
Inference: Maximum
Likelihood, 262
Tree Inference: Bayesian
Methods, 264
Stage 5: Evaluating Trees, 266
Perspective, 268
Pitfalls, 268
Web Resources, 269
Discussion Questions, 269
Problems/Computer Lab, 269
Self-Test Quiz, 271
Suggested Reading, 272
References, 272
PART II HMlflEMHRNWil
0 Bioinformatic Approaches
to Ribonucleic Acid (RNA), 279
Introduction to RNA, 279
Noncoding RNA, 282
Noncoding RNAs in the Rfam
Database, 283
Transfer RNA, 283
Ribosomal RNA, 288
Small Nuclear RNA, 291
Small Nucleolar RNA, 292
MicroRNA, 293
Short Interfering RNA, 294
Noncoding RNAs in the UCSC
Genome and Table
Browser, 294
Introduction to Messenger RNA, 296
mRNA: Subject of Gene
Expression Studies, 300
Analysis of Gene Expression in
cDNA Libraries, 302
Pitfalls in Interpreting Expression
Data from cDNA Libraries, 308
Full-Length cDNA Projects, 308
Serial Analysis of Gene Expression
(SAGE), 309
Microarrays: Genomewide
Measurement of Gene
Expression, 312
Stage 1: Experimental Design for
Microarrays, 314
Stage 2: RNA Preparation and Probe
Preparation, 316
Stage 3: Hybridization of Labeled
Samples to DNA
Microarrays, 317
Stage 4: Image Analysis, 317
Stage 5: Data Analysis, 318
Stage 6: Biological
Confirmation, 320
Microarray Databases, 320
Further Analyses, 320
Interpretation of RNA
Analyses, 320
The Relationship of DNA,
mRNA, and Protein
Levels, 320
The Pervasive Nature of
Transcription, 321
Perspective, 322
Pitfalls, 323
Web Resources, 323
Discussion Questions, 323
Problems, 324
Self-Test Quiz, 324
Suggested Reading, 325
References, 325
I Gene Expression: Microarray
Data Analysis, 331
Introduction, 331
Microarray Data Analysis Software
and Data Sets, 334
Reproducibility of Microarray
Experiments, 335
Microarray Data Analysis:
Preprocessing, 337
Scatter Plots and MA Plots, 338
Global and Local
Normalization, 343
Accuracy and Precision, 344
Robust Multiarray Analysis
(RMA), 345
Microarray Data Analysis: Inferential
Statistics, 346
Expression Ratios, 346
Hypothesis Testing, 347
Corrections for Multiple
Comparisons, 351
Significance Analysis of
Microarrays (SAM), 351
From Mest to ANOVA, 353
Microarray Data Analysis: Descriptive
Statistics, 354
Hierarchical Cluster Analysis of
Microarray Data, 355
Partitioning Methods for Clustering:
/c-Means Clustering, 363
Clustering Strategies: Self-
Organizing Maps, 363
Principal Components Analysis:
Visualizing Microarray
Data, 364
Supervised Data Analysis for
Classification of Genes or
Samples, 367
Functional Annotation of Microarray
Data, 368
Perspective, 369
Pitfalls, 370
Discussion Questions, 370
Problems/Computer Lab, 371
Self-Test Quiz, 372
Suggested Reading, 373
References, 373
ID Protein Analysis and
Proteomics, 379
Introduction, 379
Protein Databases, 380
Community Standards for
Proteomics Research, 381
Techniques to Identify Proteins, 381
Direct Protein Sequencing, 381
Gel Electrophoresis, 382
Mass Spectrometry, 385
Four Perspectives on Proteins, 388
Perspective 1. Protein Domains and
Motifs: Modular Nature of
Proteins, 389
Added Complexity of Multidomain
Proteins, 394
Protein Patterns: Motifs or
Fingerprints Characteristic of
Proteins, 394
Perspective 2. Physical Properties of
Proteins, 397
Accuracy of Prediction
Programs, 399
Proteomic Approaches to
Phosphorylation, 401
Proteomic Approaches to
Transmembrane
Domains, 401
Introduction to Perspectives 3 and 4:
Gene Ontology
Consortium, 402
Perspective 3: Protein
Localization, 406
Perspective 4: Protein
Function, 407
Perspective, 411
Pitfalls, 411
Web Resources, 412
Discussion Questions, 414
Problems/Computer Lab, 415
Self-Test Quiz, 415
Suggested Reading, 416
References, 416
11 Protein Structure, 421
Overview of Protein
Structure, 421
Protein Sequence and
Structure, 422
Biological Questions Addressed by
Structural Biology:
Globins, 423
Principles of Protein
Structure, 423
Primary Structure, 424
Secondary Structure, 425
Tertiary Protein Structure:
Protein-Folding Problem, 430
Target Selection and Acquisition
of Three-Dimensional Protein
Structures, 432
Structural Genomics and the
Protein Structure
Initiative, 432
The Protein Data Bank, 434
Accessing PDB Entries at the NCBI
Website, 437
Integrated Views of the
Universe of Protein
Folds, 441
Taxonomic System for Protein
Structures: The SCOP
Database, 441
The CATH Database, 443
The Dali Domain
Dictionary, 445
Comparison of Resources, 446
Protein Structure Prediction, 447
Homology Modeling (Comparative
Modeling), 448
Fold Recognition (Threading), 450
Ab Initio Prediction (Template-Free
Modeling), 450
A Competition to Assess
Progress in Structure
Prediction, 451
Intrinsically Disordered
Proteins, 453
Protein Structure and Disease, 453
Perspective, 454
Pitfalls, 455
Discussion Questions, 455
Problems/Computer Lab, 455
Self-Test Quiz, 456
Suggested Reading, 457
References, 457
1/ Functional Genomics, 461
Introduction to Functional
Genomics, 461
The Relationship of Genotype and
Phenotype, 463
Eight Model Organisms for
Functional Genomics, 465
The Bacterium Escherichia
coli, 466
The Yeast Saccharomyces
cerevisiae, 466
The Plant Arabidopsis
thaliana, 470
The Nematode Caenorhabditis
elegans, 470
The Fruitfly Drosophila
melanogaster, 471
The Zebraf ish Danio rerio, 471
The Mouse Mus musculus, 472
Homo sapiens: Variation in
Humans, 473
Functional Genomics Using Reverse
Genetics and Forward
Genetics, 473
Reverse Genetics: Mouse
Knockouts and the p-Globin
Gene, 475
Reverse Genetics: Knocking Out
Genes in Yeast Using Molecular
Barcodes, 480
Reverse Genetics: Random
Insertional Mutagenesis
(Gene Trapping), 483
Reverse Genetics: Insertional
Mutagenesis in Yeast, 486
Reverse Genetics: Gene
Silencing by Disrupting
RNA, 489
Forward Genetics: Chemical
Mutagenesis, 491
Functional Genomics and the Central
Dogma, 492
Functional Genomics and DNA:
The ENCODE Project, 492
Functional Genomics and
RNA, 492
Functional Genomics and
Protein, 493
Proteomics Approaches to
Functional Genomics, 493
Protein-Protein Interactions, 495
The Yeast Two-Hybrid
System, 496
Protein Complexes: Affinity
Chromatography and Mass
Spectrometry, 498
The Rosetta Stone
Approach, 500
Protein-Protein Interaction
Databases, 501
Protein Networks, 502
Perspective, 507
Pitfalls, 508
Discussion Questions, 508
Problems/Computer Lab, 509
Self-Test Quiz, 509
Suggested Reading, 510
References, 510
PART III GENOME HIS
in
Id Completed Genomes, 517
Introduction, 517
Five Perspectives on
Genomics, 519
Brief History of
Systematics, 520
History of Life on Earth, 521
Molecular Sequences as the Basis
of the Tree of Life, 523
Role of Bioinformatics in
Taxonomy, 524
Genome-Sequencing Projects:
Overview, 525
Four Prominent Web
Resources, 525
Brief Chronology, 526
First Bacteriophage and
Viral Genomes
(1976-1978), 527
First Eukaryotic Organellar
Genome (1981), 527
First Chloroplast Genomes
(1986), 528
First Eukaryotic Chromosome
(1992), 529
Complete Genome of
Free-Living Organism
(1995), 530
First Eukaryotic Genome
(1996), 532
Escherichia coli (1997), 532
First Genome of Multicellular
Organism (1998), 532
Human Chromosome
(1999), 533
Fly, Plant, and Human
Chromosome 21
(2000), 534
Draft Sequences of Human
Genome (2001), 535
Continuing Rise in Completed
Genomes (2002), 535
Expansion of Genome Projects
(2003-2009), 536
Genome Analysis Projects, 537
Criteria for Selection of Genomes
for Sequencing, 538
Genome Size, 539
Cost, 540
Relevance to Human
Disease, 541
Relevance to Basic Biological
Questions, 541
Relevance to
Agriculture, 541
Should an Individual from a
Species, Several Individuals,
or Many Individuals Be
Sequenced, 541
Resequencing Projects, 542
Ancient DNA Projects, 542
Metagenomics Projects, 543
DNA Sequencing
Technologies, 544
Sanger Sequencing, 544
Pyrosequencing, 545
Cyclic Reversible Termination:
Solexa, 547
The Process of Genome
Sequencing, 547
Genome-Sequencing
Centers, 547
Sequencing and Assembling
Genomes: Strategies, 548
Genomic Sequence Data: From
Unfinished to Finished, 549
Finishing: When Has a Genome
Been Fully Sequenced, 551
Repository for Genome
Sequence Data, 552
Role of Comparative
Genomics, 552
Genome Annotation: Features of
Genomic DNA, 555
Annotation of Genes in
Prokaryotes, 556
Annotation of Genes in
Eukaryotes, 558
Summary: Questions from
Genome-Sequencing
Projects, 558
Perspective, 559
Pitfalls, 559
Discussion Questions, 560
Problems/Computer Lab, 560
Self-Test Quiz, 560
Suggested Reading, 561
References, 561
14 Completed Genomes:
Viruses, 567
Introduction, 567
Classification of Viruses, 568
Diversity and Evolution of
Viruses, 571
Metagenomics and Virus
Diversity, 573
Bioinformatics Approaches to
Problems in Virology, 574
Influenza Virus, 574
Herpesvirus: From Phylogeny to
Gene Expression, 578
Human Immunodeficiency
Virus, 583
Bioinformatic Approaches to
HIV-1, 585
Measles Virus, 588
Perspectives, 591
Pitfalls, 591
Web Resources, 591
Discussion Questions, 592
Problems/Computer Lab, 592
Self-Test Quiz, 593
Suggested Reading, 593
References, 593
lO Completed Genomes: Bacteria
and Archaea, 597
Introduction, 598
Classification of Bacteria and
Archaea, 598
Classification of Bacteria by
Morphological Criteria, 599
Classification of Bacteria and
Archaea Based on
Genome Size and
Geometry, 602
Classification of Bacteria and
Archaea Based on
Lifestyle, 607
Classification of Bacteria Based
on Human Disease
Relevance, 610
Classification of Bacteria and
Archaea Based on Ribosomal
RNA Sequences, 611
Classification of Bacteria and
Archaea Based on Other
Molecular Sequences, 612
Analysis of Prokaryotic
Genomes, 615
Nucleotide Composition, 615
Finding Genes, 617
Lateral Gene Transfer, 620
Functional Annotation:
COGs, 622
Comparison of Prokaryotic
Genomes, 625
TaxPlot, 626
MUMmer, 628
Perspective, 629
Pitfalls, 630
Web Resources, 630
Discussion Questions, 630
Problems/Computer Lab, 631
Self-Test Quiz, 631
Suggested Reading, 632
References, 632
in
ID The Eukaryotic
Chromosome, 639
Introduction, 640
Major Differences between
Eukaryotes and
Prokaryotes, 641
General Features of Eukaryotic
Genomes and
Chromosomes, 643
C Value Paradox: Why Eukaryotic
Genome Sizes Vary So
Greatly, 643
Organization of Eukaryotic
Genomes into
Chromosomes, 644
Analysis of Chromosomes Using
Genome Browsers, 645
Analysis of Chromosomes by the
ENCODE Project, 647
Repetitive DNA Content of
Eukaryotic Chromosomes, 650
Eukaryotic Genomes Include
Noncoding and Repetitive DNA
Sequences, 650
1. Interspersed Repeats
(Transposon-Derived
Repeats), 652
2. Processed
Pseudogenes, 653
3. Simple Sequence
Repeats, 657
4. Segmental
Duplications, 658
5. Blocks of Tandemly
Repeated Sequences Such as
Are Found at Telomeres,
Centromeres, and Ribosomal
Gene Clusters, 660
Gene Content of Eukaryotic
Chromosomes, 662
Definition of Gene, 662
Finding Genes in Eukaryotic
Genomes, 663
EGASP Competition and
JIGSAW, 666
Protein-Coding Genes in
Eukaryotes: New
Paradox, 668
Regulatory Regions of Eukaryotic
Chromosomes, 669
Transcription Factor Databases
and Other Genomic DNA
Databases, 669
Ultraconserved Elements, 672
Nonconserved Elements, 673
Comparison of Eukaryotic
DNA, 673
Variation in Chromosomal
DNA, 674
Dynamic Nature of Chromosomes:
Whole Genome
Duplication, 675
Chromosomal Variation in
Individual Genomes, 676
Chromosomal Variation in
Individual Genomes:
Inversions, 678
Models for Creating Gene
Families, 678
Mechanisms of Creating
Duplications, Deletions, and
Inversions, 680
Techniques to Measure
Chromosomal Change, 682
Array Comparative Genomic
Hybridization, 682
Single Nucleotide Polymorphism
(SNP) Microarrays, 683
Perspective, 687
Pitfalls, 687
Web Resources, 688
Discussion Questions, 688
Problems/Computer Lab, 688
Self-Test Quiz, 689
Suggested Reading, 690
References, 690
I / Eukaryotic Genomes:
Fungi, 697
Introduction, 697
Description and Classification of
Fungi, 698
Introduction to Budding Yeast
Saccharomyces cenevisiae, 700
Sequencing the Yeast
Genome, 701
Features of the Budding Yeast
Genome, 701
Exploring a Typical Yeast
Chromosome, 704
Gene Duplication and Genome
Duplication of S. cerevisiae, 708
Comparative Analyses of
Hemiascomycetes, 712
Analysis of Whole Genome
Duplication, 712
Identification of Functional
Elements, 714
Analysis of Fungal Genomes, 715
Aspergillus, 715
Candida albicans, 718
Cryptococcus neoformans: Model
Fungal Pathogen, 719
Atypical Fungus: Microsporidial
Parasite Encephalitozoon
cuniculi, 719
Neurospora crassa, 719
First Basidiomycete:
Phanerochaete
chrysosporium, 720
Fission Yeast Schizosaccharomyces
pombe, 721
Perspective, 721
Pitfalls, 722
Web Resources, 722
Discussion Questions, 722
Problems/Computer Lab, 723
Self-Test Quiz, 723
Suggested Reading, 724
References, 724
18 Eukaryotic Genomes: From
Parasites to Primates, 729
Introduction, 729
Protozoans at the Base of
the Tree Lacking
Mitochondria, 732
Trichomonas, 732
Giardia lamblia: A Human
Intestinal Parasite, 733
Genomes of Unicellular Pathogens:
Trypanosomes and
Leishmania, 735
Trypanosomes, 735
Leishmania, 736
The Chromalveolates, 738
Malaria Parasite Plasmodium
falciparum and Other
Apicomplexans, 738
Astonishing Ciliophora:
Paramecium and
Tetrahymena, 742
Nucleomorphs, 745
Kingdom Stramenopila, 746
Plant Genomes, 748
Overview, 748
Green Algae (Chlorophyta), 748
Arabidopsis thaliana
Genome, 751
The Second Plant Genome:
Rice, 753
The Third Plant Genome:
Poplar, 755
The Fourth Plant Genome:
Grapevine, 755
Moss, 756
Slime and Fruiting Bodies at the
Feet of Metazoans, 756
Social Slime Mold Dictyostelium
discoideum, 756
Metazoans, 758
Introduction to
Metazoans, 758
Analysis of a Simple Animal: The
Nematode Caenorhabditis
elegans, 759
The First Insect Genome:
Drosophila melanogaster, 761
The Second Insect Genome:
Anopheles gambiae, 764
Silkworm, 765
Honeybee, 765
The Road to Chordates: The Sea
Urchin, 766
750 Million Years Ago: Ciona
intestinalis and the Road to
Vertebrates, 767
450 Million Years Ago:
Vertebrate Genomes of
Fish, 768
310 Million Years Ago: Dinosaurs
and the Chicken
Genome, 771
180 Million Years Ago: The
Opposum Genome, 772
100 Million Years Ago:
Mammalian Radiation from
Dog to Cow, 773
80 Million Years Ago: The Mouse
and Rat, 774
5 to 50 Million Years Ago:
Primate Genomes, 778
Perspective, 781
Pitfalls, 781
Web Resources, 782
Discussion Questions, 782
Problems/Computer Lab, 782
Self-Test Quiz, 783
Suggested Reading, 783
References, 784
111 Human Genome, 791
Introduction, 791
Main Conclusions of Human
Genome Project, 792
The ENCODE Project, 793
Gateways to Access the Human
Genome, 794
NCBI, 794
Ensembl, 794
University of California at Santa
Cruz Human Genome
Browser, 798
NHGRI, 800
The Wellcome Trust Sanger
Institute, 800
The Human Genome Project, 800
Background of the Human
Genome Project, 800
Strategic Issues: Hierarchical
Shotgun Sequencing to
Generate Draft
Sequence, 802
Features of the Genome
Sequence, 805
The Broad Genomic
Landscape, 806
Long-Range Variation in GC
Content, 806
CpG Islands, 807
Comparison of Genetic and
Physical Distance, 807
Repeat Content of the Human
Genome, 808
Transposon-Derived
Repeats, 809
Simple Sequence Repeats, 811
Segmental Duplications, 811
Gene Content of the Human
Genome, 811
Noncoding RNAs, 812
Protein-Coding Genes, 812
Comparative Proteome
Analysis, 814
Complexity of Human
Proteome, 814
24 Human Chromosomes, 816
Group A (Chromosomes 1, 2,
3), 818
Group B (Chromosomes 4,
5), 822
Group C (Chromosomes 6 to 12,
X), 823
Group D (Chromosomes 13 to
15), 823
Group E (Chromosomes 16 to
18), 824
Group F (Chromosomes 19,
20), 824
Group G (Chromosomes 21,
22, Y), 824
The Mitochondrial
Genome, 825
Variation: Sequencing Individual
Genomes, 825
Variation: SNPs to Copy Number
Variants, 827
Perspective, 831
Pitfalls, 831
Discussion Questions, 832
Problems/Computer Lab, 832
Self-Test Quiz, 833
Suggested Reading, 833
References, 834
nn
/U Human Disease, 839
Human Genetic Disease: A
Consequence of DNA
Variation, 839
A Bioinformatics Perspective on
Human Disease, 841
Garrod s View of Disease, 842
Classification of Disease, 843
NIH Disease Classification: MeSH
Terms, 845
Four Categories of Disease, 846
Monogenic Disorders, 847
Complex Disorders, 851
Genomic Disorders, 852
Environmentally Caused
Disease, 855
Other Categories of
Disease, 857
Disease Databases, 859
OMIM: Central Bioinformatics
Resource for Human
Disease, 859
Locus-Specific Mutation
Databases, 862
The PhenCode Project, 865
Four Approaches to Identifying
Disease-Associated Genes, 866
Linkage Analysis, 866
Genome-Wide Association
Studies, 867
Identification of Chromosomal
Abnormalities, 868
Genomic DNA Sequencing, 869
Human Disease Genes in Model
Organisms, 870
Human Disease Orthologs in
Nonvertebrate Species, 870
Human Disease Orthologs in
Rodents, 876
Human Disease Orthologs in
Primates, 878
Human Disease Genes and
Substitution Rates, 878
Functional Classification of Disease
Genes, 880
Perspective, 882
Pitfalls, 882
Web Resources, 882
Discussion Questions, 884
Problems, 884
Self-Test Quiz, 885
Suggested Reading, 885
References, 886
Glossary, 891
Answers to Self-Test Quizzes, 909
Author Index, 911
Subject Index, 913
|
| adam_txt |
Titel: Bioinformatics and functional genomics
Autor: Pevsner, Jonathan
Jahr: 2009
intents in Brie:
part i mm m. m m ran sequences in darbases
I Introduction, 3
' Access to Sequence Data and Literature Information, 13
J Pairwise Sequence Alignment, 47
i Basic Local Alignment Search Tool (BLAST), 101
3 Advanced Database Searching, 141
n
D Multiple Sequence Alignment, 1 79
/ Molecular Phylogeny and Evolution, 215
PART II GlIiEfMSIFllPIBN
o
0 Bioinformatic Approaches to Ribonucleic Acid (RNA), 279
a Gene Expression: Microarray Data Analysis, 331
lu Protein Analysis and Proteomics, 379
II Protein Structure, 421
I/ Functional Genomics, 461
PART III GENOME ANALYSIS
IJ Completed Genomes, 517
n Completed Genomes: Viruses, 567
'3 Completed Genomes: Bacteria and Archaea, 597
in
ID The Eukaryotic Chromosome, 639
1/ Eukaryotic Genomes: Fungi, 697
in
10 Eukaryotic Genomes: From Parasites to Primates, 729
lo Human Genome, 791
90
ill Human Disease, 839
Glossary, 891
Answers to Self-Test Quizzes, 909
Author Index, 911
Subject Index, 913
vii
intents
Preface to the Second Edition, xxi
Preface to the First Edition, xxiii
Foreword, xxvii
PARTI KDU1DHHKES
IN IKES
I Introduction, 3
Organization of The Book, 4
Bioinformatics: The Big Picture, 4
A Consistent Example:
Hemoglobin, 8
Organization of The Chapters, 9
A Textbook for Courses on
Bioinformatics and
Genomics, 9
Key Bioinformatics Websites, 10
Suggested Reading, 11
References, 11
/ Access to Sequence Data and
Literature Information, 13
Introduction to Biological
Databases, 13
GenBank: Database of Most Known
Nucleotide and Protein
Sequences, 14
Amount of Sequence Data, 15
Organisms in GenBank, 16
Types of Data in GenBank, 18
Genomic DNA Databases, 19
cDNA Databases Corresponding
to Expressed Genes, 19
Expressed Sequence Tags
(ESTs), 19
ESTs and UniGene, 20
Sequence-Tagged Sites
(STSs), 22
Genome Survey Sequences
(GSSs), 22
High Throughput Genomic
Sequence (HTGS), 23
Protein Databases, 23
National Center for Biotechnology
Information, 23
Introduction to NCBI: Home
Page, 23
PubMed, 23
Entrez, 24
BLAST, 25
OMIM, 25
Books, 25
Taxonomy, 25
Structure, 25
The European Bioinformatics
Institute (EBI), 25
Access to Information: Accession
Numbers to Label and Identify
Sequences, 26
The Reference Sequence (RefSeq)
Project, 27
The Consensus Coding Sequence
(CCDS) Project, 29
Access to Information via Entrez Gene
at NCBI, 29
Relationship of Entrez Gene,
Entrez Nucleotide, and Entrez
Protein, 32
Comparison of Entrez Gene and
UniGene, 32
Entrez Gene and HomoloGene, 33
Access to Information: Protein
Databases, 33
UniProt, 33
The Sequence Retrieval System at
ExPASy, 34
Access to Information: The Three
Main Genome Browsers, 35
The Map Viewer at NCBI, 35
ix
The University of California, Santa
Cruz (UCSC) Genome
Browser, 35
The Ensembl Genome Browser, 35
Examples of How to Access Sequence
Data, 36
HIV pol, 36
Histones, 38
Access to Biomedical Literature, 38
PubMed Central and Movement
toward Free Journal Access, 39
Example of PubMed Search:
RBP, 40
Perspective, 42
Pitfalls, 42
Web Resources, 42
Discussion Questions, 42
Problems, 42
Self-Test Quiz, 43
Suggested Reading, 44
References, 44
n
j Pairwise Sequence Alignment, 47
Introduction, 47
Protein Alignment: Often More
Informative Than DNA
Alignment, 47
Definitions: Homology, Similarity,
Identity, 48
Gaps, 55
Pairwise Alignment, Homology, and
Evolution of Life, 55
Scoring Matrices, 57
Dayhoff Model: Accepted Point
Mutations, 58
PAM1 Matrix, 63
PAM250 and Other PAM
Matrices, 65
From a Mutation Probability Matrix
to a Log-Odds Scoring
Matrix, 69
Practical Usefulness of PAM
Matrices in Pairwise
Alignment, 70
Important Alternative to PAM:
BLOSUM Scoring Matrices, 70
Pairwise Alignment and Limits of
Detection: The "Twilight
Zone", 74
Alignment Algorithms: Global and
Local, 75
Global Sequence Alignment:
Algorithm of Needleman and
Wunsch, 76
Step 1: Setting Up a Matrix, 76
Step 2: Scoring the Matrix, 77
Step 3: Identifying the Optimal
Alignment, 79
Local Sequence Alignment: Smith
and Waterman Algorithm, 82
Rapid, Heuristic Versions of
Smith-Waterman: FASTA and
BLAST, 84
Pairwise Alignment with Dot
Plots, 85
The Statistical Significance of Pairwise
Alignments, 86
Statistical Significance of Global
Alignments, 87
Statistical Significance of Local
Alignments, 89
Percent Identity and Relative
Entropy, 90
Perspective, 91
Pitfalls, 94
Web Resources, 94
Discussion Questions, 94
Problems/Computer Lab, 95
Self-Test Quiz, 95
Suggested Reading, 96
References, 97
4 Basic Local Alignment Search
Tool (BLAST), 101
Introduction, 101
BLAST Search Steps, 103
Step 1: Specifying Sequence of
Interest, 103
Step 2: Selecting BLAST
Program, 104
Step 3: Selecting a
Database, 106
Step 4a: Selecting Optional Search
Parameters, 106
1. Query, 107
2. Limit by Entrez Query, 107
3. Short Queries, 107
4. Expect Threshold, 107
5. Word Size, 108
6. Matrix, 110
7. Gap Penalties, 110
8. Composition-Based
Statistics, 110
9. Filtering and Masking, 111
Step 4b: Selecting Formatting
Parameters, 112
BLAST Algorithm Uses Local
Alignment Search Strategy, 115
BLAST Algorithm Parts: List, Scan,
Extend, 115
BLAST Algorithm: Local Alignment
Search Statistics and
E Value, 118
Making Sense of Raw Scores with
Bit Scores, 121
BLAST Algorithm: Relation between
E and p Values, 121
Parameters of a
BLAST Search, 123
BLAST Search Strategies, 123
General Concepts, 123
Principles of BLAST
Searching, 123
How to Evaluate Significance of
Your Results, 1 23
How to Handle Too Many
Results, 128
How to Handle Too Few
Results, 128
BLAST Searching With
Multidomain Protein: HIV-1
pol, 129
Perspective, 134
Pitfalls, 134
Web Resources, 135
Discussion Questions, 135
Computer Lab/Problems, 135
Self-Test Quiz, 136
Suggested Reading, 137
References, 137
u Advanced Database
Searching, 141
Introduction, 141
Specialized BLAST Sites, 142
Organism-Specific BLAST
Sites, 142
Ensembl BLAST, 142
Wellcome Trust Sanger
Institute, 143
Specialized BLAST-Related
Algorithms, 143
WU BLAST 2.0, 144
European Bioinformatics Institute
(EBI), 144
Specialized NCBI BLAST
Sites, 144
Finding Distantly Related Proteins:
Position-Specific Iterated BLAST
(PSI-BLAST), 145
Assessing Performance of
PSI-BLAST, 150
PSI-BLAST Errors: The Problem of
Corruption, 152
Reverse Position-Specific
BLAST, 152
Pattern-Hit Initiated BLAST
(PHI-BLAST), 153
Profile Searches: Hidden Markov
Models, 155
BLAST-Like Alignment Tools to
Search Genomic DNA
Rapidly, 161
Benchmarking to Assess Genomic
Alignment Performance, 162
PatternHunter, 162
BLASTZ, 163
MegaBLAST and Discontiguous
MegaBLAST, 164
BLAT, 166
LAGAN, 168
SSAHA, 168
SIM4, 169
Using BLAST for Gene
Discovery, 169
Perspective, 173
Pitfalls, 173
Web Resources, 174
Discussion Questions, 174
Problems/Computer Lab, 174
Self-Test Quiz, 175
Suggested Reading, 176
References, 176
n
D Multiple Sequence Alignment, 179
Introduction, 179
Definition of Multiple Sequence
Alignment, 180
Typical Uses and Practical Strategies
of Multiple Sequence
Alignment, 181
Benchmarking: Assessment of
Multiple Sequence Alignment
Algorithms, 182
Five Main Approaches to Multiple
Sequence Alignment, 184
Exact Approaches to Multiple
Sequence Alignment, 184
Progressive Sequence
Alignment, 185
Iterative Approaches, 190
Consistency-Based
Approaches, 192
Structure-Based Methods, 194
Conclusions from Benchmarking
Studies, 196
Databases of Multiple Sequence
Alignments, 197
Pfam: Protein Family Database of
Profile HMMs, 197
Smart, 199
Conserved Domain Database, 199
Prints, 201
Integrated Multiple Sequence
Alignment Resources: InterPro
and iProClass, 201
PopSet, 202
Multiple Sequence Alignment
Database Curation: Manual
versus Automated, 202
Multiple Sequence Alignments of
Genomic Regions, 203
Perspective, 206
Pitfalls, 207
Web Resources, 207
Discussion Questions, 207
Problems/Computer Lab, 208
Self-Test Quiz, 208
Suggested Reading, 209
References, 210
/ Molecular Phylogeny and
Evolution, 215
Introduction to Molecular
Evolution, 215
Goals of Molecular
Phylogeny, 216
Historical Background, 217
Molecular Clock
Hypothesis, 221
Positive and Negative
Selection, 227
Neutral Theory of Molecular
Evolution, 230
Molecular Phylogeny: Properties of
Trees, 231
Tree Roots, 233
Enumerating Trees and
Selecting Search
Strategies, 234
Type of Trees, 238
Species Trees versus Gene/Protein
Trees, 238
DNA, RNA, or Protein-Based
Trees, 240
Five Stages of Phylogenetic
Analysis, 243
Stage 1: Sequence
Acquisition, 243
Stage 2: Multiple Sequence
Alignment, 244
Stage 3: Models of DNA
and Amino Acid
Substitution, 246
Stage 4: Tree-Building
Methods, 254
Phylogenetic Methods, 255
Distance, 255
The UPGMA Distance-Based
Method, 256
Making Trees by Distance-
Based Methods: Neighbor
Joining, 259
Phylogenetic Inference: Maximum
Parsimony, 260
Model-Based Phylogenetic
Inference: Maximum
Likelihood, 262
Tree Inference: Bayesian
Methods, 264
Stage 5: Evaluating Trees, 266
Perspective, 268
Pitfalls, 268
Web Resources, 269
Discussion Questions, 269
Problems/Computer Lab, 269
Self-Test Quiz, 271
Suggested Reading, 272
References, 272
PART II HMlflEMHRNWil
0 Bioinformatic Approaches
to Ribonucleic Acid (RNA), 279
Introduction to RNA, 279
Noncoding RNA, 282
Noncoding RNAs in the Rfam
Database, 283
Transfer RNA, 283
Ribosomal RNA, 288
Small Nuclear RNA, 291
Small Nucleolar RNA, 292
MicroRNA, 293
Short Interfering RNA, 294
Noncoding RNAs in the UCSC
Genome and Table
Browser, 294
Introduction to Messenger RNA, 296
mRNA: Subject of Gene
Expression Studies, 300
Analysis of Gene Expression in
cDNA Libraries, 302
Pitfalls in Interpreting Expression
Data from cDNA Libraries, 308
Full-Length cDNA Projects, 308
Serial Analysis of Gene Expression
(SAGE), 309
Microarrays: Genomewide
Measurement of Gene
Expression, 312
Stage 1: Experimental Design for
Microarrays, 314
Stage 2: RNA Preparation and Probe
Preparation, 316
Stage 3: Hybridization of Labeled
Samples to DNA
Microarrays, 317
Stage 4: Image Analysis, 317
Stage 5: Data Analysis, 318
Stage 6: Biological
Confirmation, 320
Microarray Databases, 320
Further Analyses, 320
Interpretation of RNA
Analyses, 320
The Relationship of DNA,
mRNA, and Protein
Levels, 320
The Pervasive Nature of
Transcription, 321
Perspective, 322
Pitfalls, 323
Web Resources, 323
Discussion Questions, 323
Problems, 324
Self-Test Quiz, 324
Suggested Reading, 325
References, 325
I Gene Expression: Microarray
Data Analysis, 331
Introduction, 331
Microarray Data Analysis Software
and Data Sets, 334
Reproducibility of Microarray
Experiments, 335
Microarray Data Analysis:
Preprocessing, 337
Scatter Plots and MA Plots, 338
Global and Local
Normalization, 343
Accuracy and Precision, 344
Robust Multiarray Analysis
(RMA), 345
Microarray Data Analysis: Inferential
Statistics, 346
Expression Ratios, 346
Hypothesis Testing, 347
Corrections for Multiple
Comparisons, 351
Significance Analysis of
Microarrays (SAM), 351
From Mest to ANOVA, 353
Microarray Data Analysis: Descriptive
Statistics, 354
Hierarchical Cluster Analysis of
Microarray Data, 355
Partitioning Methods for Clustering:
/c-Means Clustering, 363
Clustering Strategies: Self-
Organizing Maps, 363
Principal Components Analysis:
Visualizing Microarray
Data, 364
Supervised Data Analysis for
Classification of Genes or
Samples, 367
Functional Annotation of Microarray
Data, 368
Perspective, 369
Pitfalls, 370
Discussion Questions, 370
Problems/Computer Lab, 371
Self-Test Quiz, 372
Suggested Reading, 373
References, 373
ID Protein Analysis and
Proteomics, 379
Introduction, 379
Protein Databases, 380
Community Standards for
Proteomics Research, 381
Techniques to Identify Proteins, 381
Direct Protein Sequencing, 381
Gel Electrophoresis, 382
Mass Spectrometry, 385
Four Perspectives on Proteins, 388
Perspective 1. Protein Domains and
Motifs: Modular Nature of
Proteins, 389
Added Complexity of Multidomain
Proteins, 394
Protein Patterns: Motifs or
Fingerprints Characteristic of
Proteins, 394
Perspective 2. Physical Properties of
Proteins, 397
Accuracy of Prediction
Programs, 399
Proteomic Approaches to
Phosphorylation, 401
Proteomic Approaches to
Transmembrane
Domains, 401
Introduction to Perspectives 3 and 4:
Gene Ontology
Consortium, 402
Perspective 3: Protein
Localization, 406
Perspective 4: Protein
Function, 407
Perspective, 411
Pitfalls, 411
Web Resources, 412
Discussion Questions, 414
Problems/Computer Lab, 415
Self-Test Quiz, 415
Suggested Reading, 416
References, 416
11 Protein Structure, 421
Overview of Protein
Structure, 421
Protein Sequence and
Structure, 422
Biological Questions Addressed by
Structural Biology:
Globins, 423
Principles of Protein
Structure, 423
Primary Structure, 424
Secondary Structure, 425
Tertiary Protein Structure:
Protein-Folding Problem, 430
Target Selection and Acquisition
of Three-Dimensional Protein
Structures, 432
Structural Genomics and the
Protein Structure
Initiative, 432
The Protein Data Bank, 434
Accessing PDB Entries at the NCBI
Website, 437
Integrated Views of the
Universe of Protein
Folds, 441
Taxonomic System for Protein
Structures: The SCOP
Database, 441
The CATH Database, 443
The Dali Domain
Dictionary, 445
Comparison of Resources, 446
Protein Structure Prediction, 447
Homology Modeling (Comparative
Modeling), 448
Fold Recognition (Threading), 450
Ab Initio Prediction (Template-Free
Modeling), 450
A Competition to Assess
Progress in Structure
Prediction, 451
Intrinsically Disordered
Proteins, 453
Protein Structure and Disease, 453
Perspective, 454
Pitfalls, 455
Discussion Questions, 455
Problems/Computer Lab, 455
Self-Test Quiz, 456
Suggested Reading, 457
References, 457
1/ Functional Genomics, 461
Introduction to Functional
Genomics, 461
The Relationship of Genotype and
Phenotype, 463
Eight Model Organisms for
Functional Genomics, 465
The Bacterium Escherichia
coli, 466
The Yeast Saccharomyces
cerevisiae, 466
The Plant Arabidopsis
thaliana, 470
The Nematode Caenorhabditis
elegans, 470
The Fruitfly Drosophila
melanogaster, 471
The Zebraf ish Danio rerio, 471
The Mouse Mus musculus, 472
Homo sapiens: Variation in
Humans, 473
Functional Genomics Using Reverse
Genetics and Forward
Genetics, 473
Reverse Genetics: Mouse
Knockouts and the p-Globin
Gene, 475
Reverse Genetics: Knocking Out
Genes in Yeast Using Molecular
Barcodes, 480
Reverse Genetics: Random
Insertional Mutagenesis
(Gene Trapping), 483
Reverse Genetics: Insertional
Mutagenesis in Yeast, 486
Reverse Genetics: Gene
Silencing by Disrupting
RNA, 489
Forward Genetics: Chemical
Mutagenesis, 491
Functional Genomics and the Central
Dogma, 492
Functional Genomics and DNA:
The ENCODE Project, 492
Functional Genomics and
RNA, 492
Functional Genomics and
Protein, 493
Proteomics Approaches to
Functional Genomics, 493
Protein-Protein Interactions, 495
The Yeast Two-Hybrid
System, 496
Protein Complexes: Affinity
Chromatography and Mass
Spectrometry, 498
The Rosetta Stone
Approach, 500
Protein-Protein Interaction
Databases, 501
Protein Networks, 502
Perspective, 507
Pitfalls, 508
Discussion Questions, 508
Problems/Computer Lab, 509
Self-Test Quiz, 509
Suggested Reading, 510
References, 510
PART III GENOME HIS
in
Id Completed Genomes, 517
Introduction, 517
Five Perspectives on
Genomics, 519
Brief History of
Systematics, 520
History of Life on Earth, 521
Molecular Sequences as the Basis
of the Tree of Life, 523
Role of Bioinformatics in
Taxonomy, 524
Genome-Sequencing Projects:
Overview, 525
Four Prominent Web
Resources, 525
Brief Chronology, 526
First Bacteriophage and
Viral Genomes
(1976-1978), 527
First Eukaryotic Organellar
Genome (1981), 527
First Chloroplast Genomes
(1986), 528
First Eukaryotic Chromosome
(1992), 529
Complete Genome of
Free-Living Organism
(1995), 530
First Eukaryotic Genome
(1996), 532
Escherichia coli (1997), 532
First Genome of Multicellular
Organism (1998), 532
Human Chromosome
(1999), 533
Fly, Plant, and Human
Chromosome 21
(2000), 534
Draft Sequences of Human
Genome (2001), 535
Continuing Rise in Completed
Genomes (2002), 535
Expansion of Genome Projects
(2003-2009), 536
Genome Analysis Projects, 537
Criteria for Selection of Genomes
for Sequencing, 538
Genome Size, 539
Cost, 540
Relevance to Human
Disease, 541
Relevance to Basic Biological
Questions, 541
Relevance to
Agriculture, 541
Should an Individual from a
Species, Several Individuals,
or Many Individuals Be
Sequenced, 541
Resequencing Projects, 542
Ancient DNA Projects, 542
Metagenomics Projects, 543
DNA Sequencing
Technologies, 544
Sanger Sequencing, 544
Pyrosequencing, 545
Cyclic Reversible Termination:
Solexa, 547
The Process of Genome
Sequencing, 547
Genome-Sequencing
Centers, 547
Sequencing and Assembling
Genomes: Strategies, 548
Genomic Sequence Data: From
Unfinished to Finished, 549
Finishing: When Has a Genome
Been Fully Sequenced, 551
Repository for Genome
Sequence Data, 552
Role of Comparative
Genomics, 552
Genome Annotation: Features of
Genomic DNA, 555
Annotation of Genes in
Prokaryotes, 556
Annotation of Genes in
Eukaryotes, 558
Summary: Questions from
Genome-Sequencing
Projects, 558
Perspective, 559
Pitfalls, 559
Discussion Questions, 560
Problems/Computer Lab, 560
Self-Test Quiz, 560
Suggested Reading, 561
References, 561
14 Completed Genomes:
Viruses, 567
Introduction, 567
Classification of Viruses, 568
Diversity and Evolution of
Viruses, 571
Metagenomics and Virus
Diversity, 573
Bioinformatics Approaches to
Problems in Virology, 574
Influenza Virus, 574
Herpesvirus: From Phylogeny to
Gene Expression, 578
Human Immunodeficiency
Virus, 583
Bioinformatic Approaches to
HIV-1, 585
Measles Virus, 588
Perspectives, 591
Pitfalls, 591
Web Resources, 591
Discussion Questions, 592
Problems/Computer Lab, 592
Self-Test Quiz, 593
Suggested Reading, 593
References, 593
lO Completed Genomes: Bacteria
and Archaea, 597
Introduction, 598
Classification of Bacteria and
Archaea, 598
Classification of Bacteria by
Morphological Criteria, 599
Classification of Bacteria and
Archaea Based on
Genome Size and
Geometry, 602
Classification of Bacteria and
Archaea Based on
Lifestyle, 607
Classification of Bacteria Based
on Human Disease
Relevance, 610
Classification of Bacteria and
Archaea Based on Ribosomal
RNA Sequences, 611
Classification of Bacteria and
Archaea Based on Other
Molecular Sequences, 612
Analysis of Prokaryotic
Genomes, 615
Nucleotide Composition, 615
Finding Genes, 617
Lateral Gene Transfer, 620
Functional Annotation:
COGs, 622
Comparison of Prokaryotic
Genomes, 625
TaxPlot, 626
MUMmer, 628
Perspective, 629
Pitfalls, 630
Web Resources, 630
Discussion Questions, 630
Problems/Computer Lab, 631
Self-Test Quiz, 631
Suggested Reading, 632
References, 632
in
ID The Eukaryotic
Chromosome, 639
Introduction, 640
Major Differences between
Eukaryotes and
Prokaryotes, 641
General Features of Eukaryotic
Genomes and
Chromosomes, 643
C Value Paradox: Why Eukaryotic
Genome Sizes Vary So
Greatly, 643
Organization of Eukaryotic
Genomes into
Chromosomes, 644
Analysis of Chromosomes Using
Genome Browsers, 645
Analysis of Chromosomes by the
ENCODE Project, 647
Repetitive DNA Content of
Eukaryotic Chromosomes, 650
Eukaryotic Genomes Include
Noncoding and Repetitive DNA
Sequences, 650
1. Interspersed Repeats
(Transposon-Derived
Repeats), 652
2. Processed
Pseudogenes, 653
3. Simple Sequence
Repeats, 657
4. Segmental
Duplications, 658
5. Blocks of Tandemly
Repeated Sequences Such as
Are Found at Telomeres,
Centromeres, and Ribosomal
Gene Clusters, 660
Gene Content of Eukaryotic
Chromosomes, 662
Definition of Gene, 662
Finding Genes in Eukaryotic
Genomes, 663
EGASP Competition and
JIGSAW, 666
Protein-Coding Genes in
Eukaryotes: New
Paradox, 668
Regulatory Regions of Eukaryotic
Chromosomes, 669
Transcription Factor Databases
and Other Genomic DNA
Databases, 669
Ultraconserved Elements, 672
Nonconserved Elements, 673
Comparison of Eukaryotic
DNA, 673
Variation in Chromosomal
DNA, 674
Dynamic Nature of Chromosomes:
Whole Genome
Duplication, 675
Chromosomal Variation in
Individual Genomes, 676
Chromosomal Variation in
Individual Genomes:
Inversions, 678
Models for Creating Gene
Families, 678
Mechanisms of Creating
Duplications, Deletions, and
Inversions, 680
Techniques to Measure
Chromosomal Change, 682
Array Comparative Genomic
Hybridization, 682
Single Nucleotide Polymorphism
(SNP) Microarrays, 683
Perspective, 687
Pitfalls, 687
Web Resources, 688
Discussion Questions, 688
Problems/Computer Lab, 688
Self-Test Quiz, 689
Suggested Reading, 690
References, 690
I / Eukaryotic Genomes:
Fungi, 697
Introduction, 697
Description and Classification of
Fungi, 698
Introduction to Budding Yeast
Saccharomyces cenevisiae, 700
Sequencing the Yeast
Genome, 701
Features of the Budding Yeast
Genome, 701
Exploring a Typical Yeast
Chromosome, 704
Gene Duplication and Genome
Duplication of S. cerevisiae, 708
Comparative Analyses of
Hemiascomycetes, 712
Analysis of Whole Genome
Duplication, 712
Identification of Functional
Elements, 714
Analysis of Fungal Genomes, 715
Aspergillus, 715
Candida albicans, 718
Cryptococcus neoformans: Model
Fungal Pathogen, 719
Atypical Fungus: Microsporidial
Parasite Encephalitozoon
cuniculi, 719
Neurospora crassa, 719
First Basidiomycete:
Phanerochaete
chrysosporium, 720
Fission Yeast Schizosaccharomyces
pombe, 721
Perspective, 721
Pitfalls, 722
Web Resources, 722
Discussion Questions, 722
Problems/Computer Lab, 723
Self-Test Quiz, 723
Suggested Reading, 724
References, 724
18 Eukaryotic Genomes: From
Parasites to Primates, 729
Introduction, 729
Protozoans at the Base of
the Tree Lacking
Mitochondria, 732
Trichomonas, 732
Giardia lamblia: A Human
Intestinal Parasite, 733
Genomes of Unicellular Pathogens:
Trypanosomes and
Leishmania, 735
Trypanosomes, 735
Leishmania, 736
The Chromalveolates, 738
Malaria Parasite Plasmodium
falciparum and Other
Apicomplexans, 738
Astonishing Ciliophora:
Paramecium and
Tetrahymena, 742
Nucleomorphs, 745
Kingdom Stramenopila, 746
Plant Genomes, 748
Overview, 748
Green Algae (Chlorophyta), 748
Arabidopsis thaliana
Genome, 751
The Second Plant Genome:
Rice, 753
The Third Plant Genome:
Poplar, 755
The Fourth Plant Genome:
Grapevine, 755
Moss, 756
Slime and Fruiting Bodies at the
Feet of Metazoans, 756
Social Slime Mold Dictyostelium
discoideum, 756
Metazoans, 758
Introduction to
Metazoans, 758
Analysis of a Simple Animal: The
Nematode Caenorhabditis
elegans, 759
The First Insect Genome:
Drosophila melanogaster, 761
The Second Insect Genome:
Anopheles gambiae, 764
Silkworm, 765
Honeybee, 765
The Road to Chordates: The Sea
Urchin, 766
750 Million Years Ago: Ciona
intestinalis and the Road to
Vertebrates, 767
450 Million Years Ago:
Vertebrate Genomes of
Fish, 768
310 Million Years Ago: Dinosaurs
and the Chicken
Genome, 771
180 Million Years Ago: The
Opposum Genome, 772
100 Million Years Ago:
Mammalian Radiation from
Dog to Cow, 773
80 Million Years Ago: The Mouse
and Rat, 774
5 to 50 Million Years Ago:
Primate Genomes, 778
Perspective, 781
Pitfalls, 781
Web Resources, 782
Discussion Questions, 782
Problems/Computer Lab, 782
Self-Test Quiz, 783
Suggested Reading, 783
References, 784
111 Human Genome, 791
Introduction, 791
Main Conclusions of Human
Genome Project, 792
The ENCODE Project, 793
Gateways to Access the Human
Genome, 794
NCBI, 794
Ensembl, 794
University of California at Santa
Cruz Human Genome
Browser, 798
NHGRI, 800
The Wellcome Trust Sanger
Institute, 800
The Human Genome Project, 800
Background of the Human
Genome Project, 800
Strategic Issues: Hierarchical
Shotgun Sequencing to
Generate Draft
Sequence, 802
Features of the Genome
Sequence, 805
The Broad Genomic
Landscape, 806
Long-Range Variation in GC
Content, 806
CpG Islands, 807
Comparison of Genetic and
Physical Distance, 807
Repeat Content of the Human
Genome, 808
Transposon-Derived
Repeats, 809
Simple Sequence Repeats, 811
Segmental Duplications, 811
Gene Content of the Human
Genome, 811
Noncoding RNAs, 812
Protein-Coding Genes, 812
Comparative Proteome
Analysis, 814
Complexity of Human
Proteome, 814
24 Human Chromosomes, 816
Group A (Chromosomes 1, 2,
3), 818
Group B (Chromosomes 4,
5), 822
Group C (Chromosomes 6 to 12,
X), 823
Group D (Chromosomes 13 to
15), 823
Group E (Chromosomes 16 to
18), 824
Group F (Chromosomes 19,
20), 824
Group G (Chromosomes 21,
22, Y), 824
The Mitochondrial
Genome, 825
Variation: Sequencing Individual
Genomes, 825
Variation: SNPs to Copy Number
Variants, 827
Perspective, 831
Pitfalls, 831
Discussion Questions, 832
Problems/Computer Lab, 832
Self-Test Quiz, 833
Suggested Reading, 833
References, 834
nn
/U Human Disease, 839
Human Genetic Disease: A
Consequence of DNA
Variation, 839
A Bioinformatics Perspective on
Human Disease, 841
Garrod's View of Disease, 842
Classification of Disease, 843
NIH Disease Classification: MeSH
Terms, 845
Four Categories of Disease, 846
Monogenic Disorders, 847
Complex Disorders, 851
Genomic Disorders, 852
Environmentally Caused
Disease, 855
Other Categories of
Disease, 857
Disease Databases, 859
OMIM: Central Bioinformatics
Resource for Human
Disease, 859
Locus-Specific Mutation
Databases, 862
The PhenCode Project, 865
Four Approaches to Identifying
Disease-Associated Genes, 866
Linkage Analysis, 866
Genome-Wide Association
Studies, 867
Identification of Chromosomal
Abnormalities, 868
Genomic DNA Sequencing, 869
Human Disease Genes in Model
Organisms, 870
Human Disease Orthologs in
Nonvertebrate Species, 870
Human Disease Orthologs in
Rodents, 876
Human Disease Orthologs in
Primates, 878
Human Disease Genes and
Substitution Rates, 878
Functional Classification of Disease
Genes, 880
Perspective, 882
Pitfalls, 882
Web Resources, 882
Discussion Questions, 884
Problems, 884
Self-Test Quiz, 885
Suggested Reading, 885
References, 886
Glossary, 891
Answers to Self-Test Quizzes, 909
Author Index, 911
Subject Index, 913 |
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| author | Pevsner, Jonathan |
| author_facet | Pevsner, Jonathan |
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| dewey-sort | 3572.8 16 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| discipline_str_mv | Biologie |
| edition | 2. ed. |
| format | Book |
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| id | DE-604.BV035162037 |
| illustrated | Illustrated |
| index_date | 2024-07-02T22:51:06Z |
| indexdate | 2024-07-09T21:26:24Z |
| institution | BVB |
| isbn | 9780470085851 |
| language | English |
| lccn | 2008040259 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016969128 |
| oclc_num | 253189041 |
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| owner_facet | DE-20 DE-29T DE-703 DE-11 |
| physical | XXVIII, 951 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Wiley-Blackwell |
| record_format | marc |
| spelling | Pevsner, Jonathan Verfasser aut Bioinformatics and functional genomics Jonathan Pevsner 2. ed. Hoboken, N.J. Wiley-Blackwell 2009 XXVIII, 951 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bioinformática larpcal Genomas (processamento de dados) larpcal Genomics Bioinformatics Proteomics Computational Biology methods Genetic Techniques Proteine (DE-588)4076388-2 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 s DE-604 Nucleinsäuren (DE-588)4172117-2 s Proteine (DE-588)4076388-2 s Genanalyse (DE-588)4200230-8 s b DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016969128&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Pevsner, Jonathan Bioinformatics and functional genomics Bioinformática larpcal Genomas (processamento de dados) larpcal Genomics Bioinformatics Proteomics Computational Biology methods Genetic Techniques Proteine (DE-588)4076388-2 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd Nucleinsäuren (DE-588)4172117-2 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4531334-9 (DE-588)4172117-2 (DE-588)4200230-8 |
| title | Bioinformatics and functional genomics |
| title_auth | Bioinformatics and functional genomics |
| title_exact_search | Bioinformatics and functional genomics |
| title_exact_search_txtP | Bioinformatics and functional genomics |
| title_full | Bioinformatics and functional genomics Jonathan Pevsner |
| title_fullStr | Bioinformatics and functional genomics Jonathan Pevsner |
| title_full_unstemmed | Bioinformatics and functional genomics Jonathan Pevsner |
| title_short | Bioinformatics and functional genomics |
| title_sort | bioinformatics and functional genomics |
| topic | Bioinformática larpcal Genomas (processamento de dados) larpcal Genomics Bioinformatics Proteomics Computational Biology methods Genetic Techniques Proteine (DE-588)4076388-2 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd Nucleinsäuren (DE-588)4172117-2 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Bioinformática Genomas (processamento de dados) Genomics Bioinformatics Proteomics Computational Biology methods Genetic Techniques Proteine Molekulare Bioinformatik Nucleinsäuren Genanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016969128&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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