Comparative Genomics : Volume 2 - Bergman, Nicholas H.; SpringerLink (Online service) (Totowa, NJ : Humana Press : Imprint: Humana, 2007)
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 GeneChip 2.0 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.
Keywords: Biochemistry; Human genetics; Cell biology; Biochemistry, general; Human Genetics; Cell Biology