Comparative Genomics: Methods and Protocols

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. Front Matter ....Pages i-xii Gene Phylogenies and Orthologous Groups (João C. Setubal, Peter F. Stadler)....Pages 1-28 Pan-Genome Storage and Analysis Techniques (Tina Zekic, Guillaume Holley, Jens Stoye)....Pages 29-53 Comparative Genomics for Prokaryotes (João C. Setubal, Nalvo F. Almeida, Alice R. Wattam)....Pages 55-78 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 et al.)....Pages 79-101 Phylogenomics (José S. L. Patané, Joaquim Martins Jr., João C. Setubal)....Pages 103-187 Comparative Genome Annotation (Stefanie König, Lars Romoth, Mario Stanke)....Pages 189-212 A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes (Danillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, Alessandro M. Varani)....Pages 213-242 Comparative Metagenomics (Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias-Neto, João C. Setubal)....Pages 243-260 Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches (Tom Hartmann, Martin Middendorf, Matthias Bernt)....Pages 261-289 Whole Genome Duplication in Plants: Implications for Evolutionary Analysis (David Sankoff, Chunfang Zheng)....Pages 291-315 Sequence-Based Synteny Analysis of Multiple Large Genomes (Daniel Doerr, Bernard M. E. Moret)....Pages 317-329 Family-Free Genome Comparison (Daniel Doerr, Pedro Feijão, Jens Stoye)....Pages 331-342 Comparative Methods for Reconstructing Ancient Genome Organization (Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve)....Pages 343-362 Comparative RNA Genomics (Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler)....Pages 363-400 Bioinformatic Approaches for Comparative Analysis of Viruses (Deyvid Amgarten, Chris Upton)....Pages 401-417 Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes (Christian Rödelsperger)....Pages 419-432 Comparative Genomics in Drosophila (Martin Oti, Attilio Pane, Michael Sammeth)....Pages 433-450 Comparative Genomics in Homo sapiens (Martin Oti, Michael Sammeth)....Pages 451-472 Back Matter ....Pages 473-481