Description
Humana Press Inc. Comparative Genomics Volume 2 by Nicholas H. Bergman
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._x000D_ _x000D_
Comparative Genomics-Volume II_x000D_
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Table of Contents_x000D_
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Section V-Comparative Analysis of Domain and Protein Families_x000D_
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1. Computational Prediction of Domain Interactions_x000D_
Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stumpflen,_x000D_
and Dmitrij Frishman_x000D_
2. DomainTeam: Synteny of domains is a new approach in comparative_x000D_
genomics_x000D_
Sophie Pasek_x000D_
3. Inference of gene function based on gene fusion events: the Rosetta_x000D_
Stone method_x000D_
Karsten Suhre_x000D_
4. Pfam: A domain-centric method for analyzing proteins and proteomes_x000D_
Jaina Mistry and Robert Finn_x000D_
5. InterPro and InterProScan-Tools for Protein Sequence Classification_x000D_
and Comparison_x000D_
Nicola Mulder and Rolf Apweiler_x000D_
6. Gene Annotation and Pathway Mapping in KEGG_x000D_
Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa_x000D_
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Section VI-Orthologs, Synteny, and Genome Evolution_x000D_
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7. Ortholog Detection using the Smallest Distance Algorithm_x000D_
Dennis P. Wall and Todd DeLuca_x000D_
8. Finding Conserved Gene Order Across Multiple Genomes_x000D_
Giulio Pavesi and Graziano Pesole_x000D_
9. Analysis of Genome Rearrangement by Block-Interchanges_x000D_
Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang_x000D_
10. Analyzing Patterns of microbial evolution using the Mauve Genome_x000D_
Alignment System_x000D_
Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T._x000D_
Perna_x000D_
11. Visualization of syntenic relationships with SynBrowse_x000D_
Volker Brendel, Stefan Kurtz, and Xiaohang Pan_x000D_
12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detection_x000D_
in Prokaryotic Genomes_x000D_
Thomas Schmidt and Jens Stoye_x000D_
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Section VII-Experimental Analysis of Whole Genomes-Analysis of Copy_x000D_
Number and Sequence Polymorphisms_x000D_
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13. Genome-wide copy number analysis on GeneChip platform using CNAG_x000D_
2.0 software_x000D_
Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto_x000D_
14. Oligonucleotide array comparative genomic hybridization_x000D_
Paul van den IJssel and Bauke Ylstra_x000D_
15. StudyingBacterial Genome Dynamics Using Microarray-Based_x000D_
Comparative Genomic Hybridization_x000D_
Eduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash_x000D_
16. CGH analysis using the CGHAnalyzer_x000D_
Joel Greshock_x000D_
17. Microarray-based Approach for Genome-Wide Survey of Nucleotide_x000D_
Polymorphisms_x000D_
Brian W. Brunelle and Tracy L. Nicholson_x000D_
18. High-Throughput Genotyping of Single Nucleotide Polymorphisms with_x000D_
High Sensitivity_x000D_
Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu,_x000D_
Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and_x000D_
Richeng Gao_x000D_
19. Single nucleotide polymorphism (SNP) mapping array assay_x000D_
Xiaofeng Zhou and David T. W. Wong_x000D_
20. Molecular Inversion Probe Assays_x000D_
Farnaz Absalan and Mostafa Ronaghi_x000D_
21. novoSNP: variant detection and sequence annotation in resequencing_x000D_
projects_x000D_
Peter De Rijk and Jurgen Del-Favero_x000D_
22. Rapid Identification of Single Nucleotide Substitutions Using_x000D_
SeqDoc_x000D_
Mark L. Crowe_x000D_
23. SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing_x000D_
Single Nucleotide Polymorphisms_x000D_
Tianhua Niu_x000D_
24. Identification of Disease Genes: An Example-driven Web-based_x000D_
Tutorial_x000D_
Medha Bhagwat_x000D_
25. Variable number tandem repeat typing of bacteria_x000D_
Siamak P. Yazdankhah and Bjorn-Arne Lindstedt_x000D_
26. Fluorescent amplified fragment length polymorphism (FAFLP)_x000D_
genotyping of bacterial species_x000D_
Meeta Desai_x000D_
27. FLP-mapping: A universal, cost-effective, and automatable method_x000D_
for gene mapping_x000D_
Knud Nairz, Peder Zipperlen, and Manuel Schneider_x000D_