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.
|Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Preface...
Table of Contents...
Contributing Authors...
1. Gene Phyologenies and Orthologous Groups
João 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
João 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 João C. Setubal
6. Comparative Genome Annotation
Stefanie König, 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 João 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 Feijão, and Jens Stoye
13. Comparative Methods for Reconstructing Ancient Genome Organization
Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, 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 Rödelsperger
17. Comparative Genomics in Drosophila
Martin Oti, attilio Pane, and Michael Sammeth
18. Comparative Genomics in Human
Martin Oti and Michael Sammeth
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.
Gene Phyologenies and Orthologous Groups.- Pan-Genome Storage and Analysis Techniques.- Comparative Genomics for Prokaryotes.- Assembly, Annotation and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.- Phylogenomics.- Comparative Genome Annotation.- A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes.- Comparative Metagenomics.- Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.- Whole Genome Duplications in Plants; Implications for Evolutionary Analysis.- Sequence-Based Synteny Analysis of Multiple Large Genomes.- Family-Free Genome Comparison.- Comparative Methods for Reconstructing Ancient Genome Organization.- Comparative RNA Genomics.- Bioinformatic Approached for Comparative Analysis of Viruses.- Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes.- Comparative Genomics in Drosophila.- Comparative Genomics in Human.
Inhaltsverzeichnis
Gene Phyologenies and Orthologous Groups.- Pan-Genome Storage and Analysis Techniques.- Comparative Genomics for Prokaryotes.- Assembly, Annotation and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.- Phylogenomics.- Comparative Genome Annotation.- A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes.- Comparative Metagenomics.- Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.- Whole Genome Duplications in Plants; Implications for Evolutionary Analysis.- Sequence-Based Synteny Analysis of Multiple Large Genomes.- Family-Free Genome Comparison.- Comparative Methods for Reconstructing Ancient Genome Organization.- Comparative RNA Genomics.- Bioinformatic Approached for Comparative Analysis of Viruses.- Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes.- Comparative Genomics in Drosophila.- Comparative Genomics in Human.
Klappentext
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.nnCutting-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.
n
Includes cutting-edge methods and protocols
rn
Provides step-by-step detail essential for reproducible results
rn
Contains key notes and implementation advice from the experts
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