Comparative Genomics

Editors:

ISBN: 978-1-58829-693-1 (Print) 978-1-59745-514-5 (Online)

Table of contents (33 protocols)

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  1. Front Matter

    Pages i-xiv

  2. Genome Visualization and Annotation

    1. Front Matter

      Pages 1-1

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      Book Protocol

      Pages 3-16

      Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools

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      Book Protocol

      Pages 17-33

      Comparative Genomic Analysis Using the UCSC Genome Browser

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      Pages 35-56

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

    5. No Access

      Book Protocol

      Pages 57-74

      WebACT

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      Pages 75-96

      GenColors

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      Book Protocol

      Pages 97-108

      Comparative Microbial Genome Visualization Using GenomeViz

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      Pages 109-132

      BugView

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      Pages 133-146

      CGAS

  3. Sequence Alignments

    1. Front Matter

      Pages 147-147

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      Book Protocol

      Pages 149-175

      BLAST QuickStart

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      Book Protocol

      Pages 177-186

      PSI-BLAST Tutorial

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      Book Protocol

      Pages 187-194

      Organizing and Updating Whole Genome BLAST Searches with ReHAB

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      Pages 195-203

      Alignment of Genomic Sequences Using DIALIGN

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      Pages 205-219

      An Introduction to the Lagan Alignment Toolkit

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      Pages 221-235

      Aligning Multiple Whole Genomes with Mercator and MAVID

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      Pages 237-253

      Mulan

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      Pages 255-268

      Improving Pairwise Sequence Alignment between Distantly Related Proteins

  4. Identification of Conserved Sequences and Biases in Codon Usage

    1. Front Matter

      Pages 269-269

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      Book Protocol

      Pages 271-292

      Discovering Sequence Motifs

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      Pages 293-308

      Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

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      Pages 309-317

      PhyME

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      Pages 319-328

      Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool

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