This volume provides broad coverage of computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. Written in the highly successful Methods in Molecular Biology series format, by authors who are active researchers in the field, many chapters include step-by-step procedures, which illustrate practical applications of the techniques described.Cutting-edge and thorough, Comparative Genomics: Methods and Protocols should be useful to students and researchers in the continually growing and exciting field of comparative genomics.
Preface...Table of Contents...Contributing Authors...1. Gene Phyologenies and Orthologous GroupsJoao C. Setubal and Peter F. Stadler2. Pan-Genome Storage and Analysis TechniquesTina Zekic, Guillaume Holley, and Jens Stoye3. Comparative Genomics for ProkaryotesJoao C. Setubal, Nalvo Almeida, and Alice R. Wattam4. Assembly, Annotation and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource CenterAlice R. Wattam, Thomas Brettin, James J. Davis, Svetlana Gerdes, Ronald Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik P. Shukla, Rick Stevens, Veronika Vonstein, Andrew Warren, Fangfang Xia, and Hyunseung Yoo5. PhylogenomicsJose S. L. Patane, Joaquim Martins Jr., and Joao C. Setubal6. Comparative Genome Annotation7. A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic GenomesDanillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, and Alessandro M. Varani8. Comparative MetagenomicsAndrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias Neto, and Joao C. Setubal9. Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving ApproachesTom Hartmann, Martin Middendorf, and Matthias Bernt10. Whole Genome Duplications in Plants; Implications for Evolutionary AnalysisDavid Sankoff and Chunfang Zheng11. Sequence-Based Synteny Analysis of Multiple Large GenomesDaniel Doerr and Bernard M.E. Moret12. Family-Free Genome ComparisonDaniel Doerr, Pedro Feijao, and Jens Stoye13. Comparative Methods for Reconstructing Ancient Genome OrganizationYoann Anselmetti, Nina Luhmann, Severine Berard, Eric Tannier, and Cedric Chauve14. Comparative RNA GenomicsRolf Backofen, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler15. Bioinformatic Approached for Comparative Analysis of VirusesDeyvid Amgarten and Chris Upton16. Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other NematodesChristian Rodelsperger17. Comparative Genomics in DrosophilaMartin Oti, attilio Pane, and Michael Sammeth 18. Comparative Genomics in HumanMartin Oti and Michael Sammeth