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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
    2. Timothy L. Bailey
      Pages 271-292
    3. Rekin’s Janky, Jacques van Helden
      Pages 293-308
    4. Saurabh Sinha
      Pages 309-317
    5. Olivier Sand, Jacques van Helden
      Pages 329-347
    6. Olivier Elemento, Saeed Tavazoie
      Pages 349-366
    7. Austen R.D. Ganley, Takehiko Kobayashi
      Pages 367-379
    8. Rahul Siddharthan, Erik van Nimwegen
      Pages 381-402
    9. William Thompson, Sean Conlan, Lee Ann McCue, Charles E. Lawrence
      Pages 403-423
    10. Panayiotis V. Benos, David L. Corcoran, Eleanor Feingold
      Pages 425-436
    11. Eugene Berezikov, Victor Guryev, Edwin Cuppen
      Pages 437-448
    12. Gabriela Moura, Miguel Pinheiro, Adelaide Valente Freitas, José Luís Oliveira, Manuel A. S. Santos
      Pages 449-462
  5. Identification and Structural Characterization of Noncoding RNAs

  6. Back Matter
    Pages 545-546

About this book

Introduction

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.

Keywords

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 https://doi.org/10.1007/978-1-59745-514-5
  • 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
  • Buy this book on publisher's site