Table of Contents
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
