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Comparative Genomics

Volume 1

  • Book
  • © 2008

Overview

Editors:
  1. Nicholas H. Bergman

    1. Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor

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  • Provides a collection of robust protocols for molecular biologists studying comparative genomics
  • Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique
  • A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently

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

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Table of contents (33 protocols)

  1. Front Matter

    Pages i-xiv
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  2. Genome Visualization and Annotation

    1. Front Matter

      Pages 1-1
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    2. Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools

      • Inna Dubchak
      Pages 3-16

    3. Comparative Genomic Analysis Using the UCSC Genome Browser

      • Donna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb Miller, Kate R. Rosenbloom et al.
      Pages 17-33

    4. Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System

      • Victor M. Markowitz, Nikos C. Kyrpides
      Pages 35-56

    5. WebACT

      • James C. Abbott, David M. Aanensen, Stephen D. Bentley
      Pages 57-74

    6. GenColors

      • Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glöckner et al.
      Pages 75-96

    7. Comparative Microbial Genome Visualization Using GenomeViz

      • Rohit Ghai, Trinad Chakraborty
      Pages 97-108

    8. BugView

      • David P. Leader
      Pages 109-132

    9. CGAS

      • Kwangmin Choi, Youngik Yang, Sun Kim
      Pages 133-146

  3. Sequence Alignments

    1. Front Matter

      Pages 147-147
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    2. BLAST QuickStart

      • David Wheeler, Medha Bhagwat
      Pages 149-175

    3. PSI-BLAST Tutorial

      • Medha Bhagwat, L. Aravind
      Pages 177-186

    4. Organizing and Updating Whole Genome BLAST Searches with ReHAB

      • David J Esteban, Aijazuddin Syed, Chris Upton
      Pages 187-194

    5. Alignment of Genomic Sequences Using DIALIGN

      • Burkhard Morgenstern
      Pages 195-203

    6. An Introduction to the Lagan Alignment Toolkit

      • Michael Brudno
      Pages 205-219

    7. Aligning Multiple Whole Genomes with Mercator and MAVID

      • Colin N. Dewey
      Pages 221-235

    8. Mulan

      • Gabriela G. Loots, Ivan Ovcharenko
      Pages 237-253

    9. Improving Pairwise Sequence Alignment between Distantly Related Proteins

      • Jin-an Feng
      Pages 255-268

  4. Identification of Conserved Sequences and Biases in Codon Usage

    1. Front Matter

      Pages 269-269
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Keywords

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.

Editors and Affiliations

  • Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor

    Nicholas H. Bergman

Bibliographic Information

  • Book Title: Comparative Genomics

  • Book Subtitle: Volume 1

  • Editors: Nicholas H. Bergman

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-514-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-693-1Published: 29 November 2007

  • Softcover ISBN: 978-1-61737-722-8Published: 25 December 2011

  • eBook ISBN: 978-1-59745-514-5Published: 29 June 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 546

  • Number of Illustrations: 144 b/w illustrations, 3 illustrations in colour

  • Topics: Biochemistry, general, Human Genetics, Cell Biology

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