Comparative Genomics: Methods and Protocols

ISBN-13: 9781493974610 / Angielski / Twarda / 2017 / 481 str.

Joao C. Setubal; Jens Stoye; Peter F. Stadler

Opis

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.

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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