Comparative Genomics

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