Description
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 Groups Joo C. Setubal and Peter F. Stadler 2. Pan-Genome Storage and Analysis Techniques Tina Zekic, Guillaume Holley, and Jens Stoye 3. Comparative Genomics for Prokaryotes Joo C. Setubal, Nalvo Almeida, and Alice R. Wattam 4. Assembly, Annotation and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center Alice 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 Yoo 5. Phylogenomics Jose S. L. Patane, Joaquim Martins Jr., and Joo C. Setubal 6. Comparative Genome Annotation Stefanie Knig, Lars Romoth, and Mario Stanke 7. A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes Danillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, and Alessandro M. Varani 8. Comparative Metagenomics Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias Neto, and Joo C. Setubal 9. Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches Tom Hartmann, Martin Middendorf, and Matthias Bernt 10. Whole Genome Duplications in Plants; Implications for Evolutionary Analysis David Sankoff and Chunfang Zheng 11. Sequence-Based Synteny Analysis of Multiple Large Genomes Daniel Doerr and Bernard M.E. Moret 12. Family-Free Genome Comparison Daniel Doerr, Pedro Feijo, and Jens Stoye 13. Comparative Methods for Reconstructing Ancient Genome Organization Yoann Anselmetti, Nina Luhmann, Sverine Brard, Eric Tannier, and Cedric Chauve 14. Comparative RNA Genomics Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler 15. Bioinformatic Approached for Comparative Analysis of Viruses Deyvid Amgarten and Chris Upton 16. Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes Christian Rdelsperger 17. Comparative Genomics in Drosophila Martin Oti, attilio Pane, and Michael Sammeth 18. Comparative Genomics in Human Martin Oti and Michael Sammeth
