Preface |
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v | |
Contributors |
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xi | |
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Table of Contents---Volume 1 |
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xv | |
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PART I: COMPARATIVE ANALYSIS OF DOMAIN AND PROTEIN FAMILIES |
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Computational Prediction of Domain Interactions |
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3 | (14) |
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Domain Team: Synteny of Domains is a New Approach in Comparative Genomics |
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17 | (14) |
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Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method |
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31 | (12) |
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Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes |
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43 | (16) |
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InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison |
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59 | (12) |
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Gene Annotation and Pathway Mapping in KEGG |
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71 | (24) |
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PART II: ORTHOLOGS, SYNTENY, AND GENOME EVOLUTION |
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Ortholog Detection Using the Reciprocal Smallest Distance Algorithm |
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95 | (16) |
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Finding Conserved Gene Order Across Multiple Genomes |
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111 | (10) |
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Analysis of Genome Rearrangement by Block-Interchanges |
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121 | (14) |
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Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System |
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135 | (18) |
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Visualization of Syntenic Relationships With SynBrowse |
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153 | (12) |
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Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes |
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165 | (20) |
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PART III: EXPERIMENTAL ANALYSIS OF WHOLE GENOMES: ANALYSIS OF COPY NUMBER AND SEQUENCE POLYMORPHISMS |
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Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software |
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185 | (22) |
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Oligonucleotide Array Comparative Genomic Hybridization |
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207 | (16) |
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Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization |
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223 | (32) |
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DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite |
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255 | (12) |
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Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms |
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267 | (14) |
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High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity |
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281 | (14) |
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Single Nucleotide Polymorphism Mapping Array Assay |
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295 | (20) |
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Molecular Inversion Probe Assay |
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315 | (16) |
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novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects |
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331 | (14) |
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Rapid Identification of Single Nucleotide Substitutions Using SeqDoC |
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345 | (14) |
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SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms |
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359 | (12) |
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Identification of Disease Genes: Example-Driven Web-Based Tutorial |
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371 | (24) |
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Variable Number Tandem Repeat Typing of Bacteria |
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395 | (12) |
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Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species |
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407 | (12) |
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FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping |
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419 | (14) |
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Index |
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433 | (112) |
Preface |
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ix | |
Contributors |
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xi | |
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PART 1: GENOME VISUALIZATION AND ANNOTATION |
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1 | (146) |
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Comparative Analysis and Visualization of Genomic Sequences Using Vista Browser and Associated Computational Tools |
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3 | (14) |
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Comparative Genomic Analysis Using the UCSC Genome Browser |
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17 | (18) |
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Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System |
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35 | (22) |
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WebAct: An Online Genome Comparison Suite |
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57 | (18) |
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GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy |
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75 | (22) |
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Comparative Microbial Genome Visualization Using GenomeViz |
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97 | (12) |
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BugView: A Tool for Genome Visualization and Comparison |
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109 | (24) |
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CGAS: A Comparative Genome Annotation System |
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133 | (14) |
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PART 2: SEQUENCE ALIGNMENTS |
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147 | (122) |
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Blast QuickStart: Example-Driven Web-Based Blast Tutorial |
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149 | (28) |
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177 | (10) |
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Organizing and Updating Whole Genome Blast Searches With ReHAB |
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187 | (8) |
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Alignment of Genomic Sequences Using Dialign |
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195 | (10) |
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An Introduction to the Lagan Alignment Toolkit |
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205 | (16) |
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Aligning Multiple Whole Genomes with Mercator and Mavid |
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221 | (16) |
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Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences |
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237 | (18) |
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Improving Pairwise Sequence Alignment between Distantly Related Proteins |
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255 | (14) |
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PART 3: IDENTIFICATION OF CONSERVED SEQUENCES AND BIASES IN CODON USAGE |
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269 | (194) |
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Discovering Sequence Motifs |
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271 | (22) |
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Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes |
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293 | (16) |
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PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences |
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309 | (10) |
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Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool |
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319 | (10) |
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Discovery of Motifs in Promoters of Coregulated Genes |
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329 | (20) |
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Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation |
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349 | (18) |
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Phylogenetic Footprinting to Find Functional DNA Elements |
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367 | (14) |
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Detecting Regulatory Sites Using PhyloGibbs |
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381 | (22) |
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Using the Gibbs Motif Sampler for Phylogenetic Footprinting |
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403 | (22) |
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Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements |
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425 | (12) |
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Exploring Conservation of Transcription Factor Binding Sites with Conreal |
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437 | (12) |
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Computational and Statistical Methodologies for ORFeome Primary Structure Analysis |
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449 | (14) |
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PART 4: IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF NONCODING RNAs |
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463 | (82) |
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Comparative Analysis of RNA Genes: The caRNAc Software |
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465 | (10) |
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Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2 |
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475 | (14) |
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Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA |
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489 | (14) |
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Prediction of Structural Noncoding RNAs With RNAz |
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503 | (24) |
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RNA Consensus Structure Prediction With RNAalifold |
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527 | (18) |
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Index |
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545 | |