Comparative Genomics

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.