Provides a collection of robust protocols for molecular biologists studying comparative genomics
Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique
A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently
This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel.
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Comparative Genomics, Volume 2, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume 2 contains the last three of seven sections. In the second volume, the fifth section describes a number of tools for comparative analysis of domain and gene families. These tools are particularly useful for predicting protein function as well as potential protein-protein interactions. In the sixth section, methods for comparing groups of genes and gene order are discussed, as are several tools for analyzing genome evolution. Finally, the seventh section deals with experimental comparative genomics. This section includes methods for comparing gene copy number across an entire genome, comparative genomic hybridization, SNP analysis, as well as genome-wide mapping and typing systems for bacterial genomes. Given the tremendous increase in available biosequence data over the past ten years, Comparative Genomics, Volume 1, is timely, comprehensive, and novel. A companion Volume 1 is also available from Humana Press.
Comparative Genomics-Volume IITable of ContentsSection V-Comparative Analysis of Domain and Protein Families1. Computational Prediction of Domain InteractionsPhilipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen,and Dmitrij Frishman2. DomainTeam: Synteny of domains is a new approach in comparativegenomicsSophie Pasek3. Inference of gene function based on gene fusion events: the RosettaStone methodKarsten Suhre4. Pfam: A domain-centric method for analyzing proteins and proteomesJaina Mistry and Robert Finn5. InterPro and InterProScan-Tools for Protein Sequence Classificationand ComparisonNicola Mulder and Rolf Apweiler6. Gene Annotation and Pathway Mapping in KEGGKiyoko F. Aoki-Kinoshita and Minoru KanehisaSection VI-Orthologs, Synteny, and Genome Evolution7. Ortholog Detection using the Smallest Distance AlgorithmDennis P. Wall and Todd DeLuca8. Finding Conserved Gene Order Across Multiple GenomesGiulio Pavesi and Graziano Pesole9. Analysis of Genome Rearrangement by Block-InterchangesChin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang10. Analyzing Patterns of microbial evolution using the Mauve GenomeAlignment SystemAaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T.Perna11. Visualization of syntenic relationships with SynBrowseVolker Brendel, Stefan Kurtz, and Xiaohang Pan12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detectionin Prokaryotic GenomesThomas Schmidt and Jens StoyeSection VII-Experimental Analysis of Whole Genomes-Analysis of CopyNumber and Sequence Polymorphisms13. Genome-wide copy number analysis on GeneChip platform using CNAG2.0 softwareSeishi Ogawa, Yasuhito Nanya, and Go Yamamoto14. Oligonucleotide array comparative genomic hybridizationPaul van den IJssel and Bauke Ylstra15. StudyingBacterial Genome Dynamics Using Microarray-BasedComparative Genomic HybridizationEduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash16. CGH analysis using the CGHAnalyzerJoel Greshock17. Microarray-based Approach for Genome-Wide Survey of NucleotidePolymorphismsBrian W. Brunelle and Tracy L. Nicholson18. High-Throughput Genotyping of Single Nucleotide Polymorphisms withHigh SensitivityHonghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu,Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, andRicheng Gao19. Single nucleotide polymorphism (SNP) mapping array assayXiaofeng Zhou and David T. W. Wong20. Molecular Inversion Probe AssaysFarnaz Absalan and Mostafa Ronaghi21. novoSNP: variant detection and sequence annotation in resequencingprojectsPeter De Rijk and Jurgen Del-Favero22. Rapid Identification of Single Nucleotide Substitutions UsingSeqDocMark L. Crowe23. SNPHunter: A Versatile Web-Based Tool for Acquiring and ManagingSingle Nucleotide PolymorphismsTianhua Niu24. Identification of Disease Genes: An Example-driven Web-basedTutorialMedha Bhagwat25. Variable number tandem repeat typing of bacteriaSiamak P. Yazdankhah and Bjørn-Arne Lindstedt26. Fluorescent amplified fragment length polymorphism (FAFLP)genotyping of bacterial speciesMeeta Desai27. FLP-mapping: A universal, cost-effective, and automatable methodfor gene mappingKnud Nairz, Peder Zipperlen, and Manuel Schneider
Preface v.- Contributors xi.- Table of Contents-Volume 1 xv.- I: Comparative Analysis of Domain and Protein Families.- 1 Computational Prediction of Domain Interactions 3Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman 3.- 2 Domain Team: Synteny of Domains is a New Approach in Comparative Genomics 17Sophie Pasek 17.- 3 Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method 31Karsten Suhre 31.- 4 Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes 43Jaina Mistry and Robert Finn 43.- 5 InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison 59Nicola Mulder and Rolf Apweiler 59.- 6 Gene Annotation and Pathway Mapping in KEGG 71Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa 71.- II:Orthologs, Synteny, and Genome Evolution.- 7 Ortholog Detection Using the Reciprocal Smallest Distance Algorithm 95Dennis P. Wall and Todd DeLuca 95.- 8 Finding Conserved Gene Order Across Multiple Genomes 111Giulio Pavesi and Graziano Pesole 111.- 9 Analysis of Genome Rearrangement by Block-Interchanges 121Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang 121.- 10 Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System 135Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T. Perna 135.- 11 Visualization of Syntenic Relationships With SynBrowse 153Volker Brendel, Stefan Kurtz, and Xioakang Pan 153.- 12 Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes 165Thomas Schmidt and Jens Stoye 165.- III:Experimental Analysis of Whole Genomes: A NALYSIS OF C OPY N UMBER AND S EQUENCE P OLYMORPHISMS.- 13 Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip2.0 Software 185Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto 185.- 14 Oligonucleotide Array Comparative Genomic Hybridization 207Paul van den IJssel and Bauke Ylstra 207.- 15 Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization 223Eduardo N. Taboada, Christian C. Luebbert, and John H. E. Nash 223.- 16 DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite 255Joel Greshock 255.- 17 Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms 267Brian W. Brunelle and Tracy L. Nicholson 267.- 18 High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity 281Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu, Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and Richeng Gao 281.- 19 Single Nucleotide Polymorphism Mapping Array Assay 295Xiaofeng Zhou and David T. W. Wong 295.- 20 Molecular Inversion Probe Assay 315Farnaz Absalan and Mostafa Ronaghi 315.- 21 novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects 331Peter De Rijk and Jurgen Del-Favero 331.- 22 Rapid Identification of Single Nucleotide Substitutions Using SeqDoC 345Mark L. Crowe 345.- 23 SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms 359Tianhua Niu 359.- 24 Identification of Disease Genes: Example-Driven Web-Based Tutorial 371Medha Bhagwat 371.- 25 Variable Number Tandem Repeat Typing of Bacteria 395Siamak P. Yazdankhah and BjØrn-Arne Lindstedt 395.- 26 Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species 405Meeta Desai 407.- 27 FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping 419Knud Nairz, Peder Zipperlen, and Manuel Schneider 419.- Index 433.
Inhaltsverzeichnis
Comparative Genomics-Volume II
Table of Contents
Section V-Comparative Analysis of Domain and Protein Families
1. Computational Prediction of Domain Interactions
Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen,
and Dmitrij Frishman
2. DomainTeam: Synteny of domains is a new approach in comparative
genomics
Sophie Pasek
3. Inference of gene function based on gene fusion events: the Rosetta
Stone method
Karsten Suhre
4. Pfam: A domain-centric method for analyzing proteins and proteomes
Jaina Mistry and Robert Finn
5. InterPro and InterProScan-Tools for Protein Sequence Classification
and Comparison
Nicola Mulder and Rolf Apweiler
6. Gene Annotation and Pathway Mapping in KEGG
Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa
Section VI-Orthologs, Synteny, and Genome Evolution
7. Ortholog Detection using the Smallest Distance Algorithm
Dennis P. Wall and Todd DeLuca
8. Finding Conserved Gene Order Across Multiple Genomes
Giulio Pavesi and Graziano Pesole
9. Analysis of Genome Rearrangement by Block-Interchanges
Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang
10. Analyzing Patterns of microbial evolution using the Mauve Genome
Alignment System
Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T.
Perna
11. Visualization of syntenic relationships with SynBrowse
Volker Brendel, Stefan Kurtz, and Xiaohang Pan
12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detection
in Prokaryotic Genomes
Thomas Schmidt and Jens Stoye
Section VII-Experimental Analysis of Whole Genomes-Analysis of Copy
Number and Sequence Polymorphisms
13. Genome-wide copy number analysis on GeneChip platform using CNAG
2.0 software
Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto
14. Oligonucleotide array comparative genomic hybridization
Paul van den IJssel and Bauke Ylstra
15. StudyingBacterial Genome Dynamics Using Microarray-Based
Comparative Genomic Hybridization
Eduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash
16. CGH analysis using the CGHAnalyzer
Joel Greshock
17. Microarray-based Approach for Genome-Wide Survey of Nucleotide
Polymorphisms
Brian W. Brunelle and Tracy L. Nicholson
18. High-Throughput Genotyping of Single Nucleotide Polymorphisms with
High Sensitivity
Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu,
Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and
Richeng Gao
19. Single nucleotide polymorphism (SNP) mapping array assay
Xiaofeng Zhou and David T. W. Wong
20. Molecular Inversion Probe Assays
Farnaz Absalan and Mostafa Ronaghi
21. novoSNP: variant detection and sequence annotation in resequencing
projects
Peter De Rijk and Jurgen Del-Favero
22. Rapid Identification of Single Nucleotide Substitutions Using
SeqDoc
Mark L. Crowe
23. SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing
Single Nucleotide Polymorphisms
Tianhua Niu
24. Identification of Disease Genes: An Example-driven Web-based
Tutorial
Medha Bhagwat
25. Variable number tandem repeat typing of bacteria
Siamak P. Yazdankhah and Bjørn-Arne Lindstedt
26. Fluorescent amplified fragment length polymorphism (FAFLP)
genotyping of bacterial species
Meeta Desai
27. FLP-mapping: A universal, cost-effective, and automatable method
for gene mapping
Knud Nairz, Peder Zipperlen, and Manuel Schneider
Klappentext
Comparative Genomics, Volume 2, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume 2 contains the last three of seven sections. In the second volume, the fifth section describes a number of tools for comparative analysis of domain and gene families. These tools are particularly useful for predicting protein function as well as potential protein-protein interactions. In the sixth section, methods for comparing groups of genes and gene order are discussed, as are several tools for analyzing genome evolution. Finally, the seventh section deals with experimental comparative genomics. This section includes methods for comparing gene copy number across an entire genome, comparative genomic hybridization, SNP analysis, as well as genome-wide mapping and typing systems for bacterial genomes. Given the tremendous increase in available biosequence data over the past ten years, Comparative Genomics, Volume 1, is timely, comprehensive, and novel. A companion Volume 1 is also available from Humana Press.
Provides a collection of robust protocols for molecular biologists studying comparative genomics
Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique
A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently
