Comparative Genomics

  • Nicholas H. Bergman

Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Table of contents

  1. Front Matter
    Pages i-xiv
  2. Genome Visualization and Annotation

    1. Front Matter
      Pages 1-1
    2. Donna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb Miller, Kate R. Rosenbloom et al.
      Pages 17-33
    3. Victor M. Markowitz, Nikos C. Kyrpides
      Pages 35-56
    4. James C. Abbott, David M. Aanensen, Stephen D. Bentley
      Pages 57-74
    5. Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glöckner et al.
      Pages 75-96
    6. Rohit Ghai, Trinad Chakraborty
      Pages 97-108
    7. David P. Leader
      Pages 109-132
    8. Kwangmin Choi, Youngik Yang, Sun Kim
      Pages 133-146
  3. Sequence Alignments

    1. Front Matter
      Pages 147-147
    2. David Wheeler, Medha Bhagwat
      Pages 149-175
    3. Medha Bhagwat, L. Aravind
      Pages 177-186
    4. David J Esteban, Aijazuddin Syed, Chris Upton
      Pages 187-194
    5. Burkhard Morgenstern
      Pages 195-203
    6. Michael Brudno
      Pages 205-219
    7. Gabriela G. Loots, Ivan Ovcharenko
      Pages 237-253
  4. Identification of Conserved Sequences and Biases in Codon Usage

    1. Front Matter
      Pages 269-269

About this book


Comparative Genomics, Volume 1, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume I contains the first four of seven sections. In the first section, the reader is introduced to genomes via a number of visualization tools that allow one to browse through a particular genome of interest. The second and third sections deal with comparative analysis at the level of individual sequences, and present methods useful in sequence alignment, the discovery of conserved sequence motifs, and the analysis of codon usage. The fourth section deals with the identification and structural characterization of non-coding RNA genes — this class of genes is particularly difficult to predict, and discovery of these elements is almost completely reliant on comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, Comparative Genomics, Volume 1, is timely, comprehensive, and novel. A companion Volume 2 is also available from Humana Press.


Bur DNA Evolution Promoter RNA conservation genes primary structure prokaryotes transcription

Editors and affiliations

  • Nicholas H. Bergman
    • 1
  1. 1.Bioinformatics Program and Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn Arbor

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2008
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-693-1
  • Online ISBN 978-1-59745-514-5
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • About this book