Comparative Genomics

Comparative Genomics : Volume 1

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This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel. The volume is intended for molecular biologists, biochemists and geneticists.
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Product details

  • Hardback | 546 pages
  • 154.94 x 231.14 x 35.56mm | 975.22g
  • Totowa, NJ, United States
  • English
  • 2008 ed.
  • 17 Tables, black and white; 3 Illustrations, color; 144 Illustrations, black and white; XIV, 546 p. 147 illus., 3 illus. in color.
  • 1588296938
  • 9781588296931

Back cover copy

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.
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Table of contents

Comparative Genomics-Volume I

Table of Contents

Section I-Genome Visualization and Annotation

1. Comparative analysis and visualization of genomic sequences using
VISTA Browser and associated computational tools
Inna Dubchak
2. Comparative Genomic Analysis Using the UCSC Genome Browser
Donna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb
Miller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent
3. Comparative Genome Analysis in the Integrated Microbial Genomes
(IMG) System
Victor M. Markowitz and Nikos C. Kyrpides
4. WebACT: An Online Genome Comparison Suite
James C. Abbott, David M. Aanensen, and Stephen D. Bentley
5. GenColors: Annotation and Comparative Genomics of Prokaryotes made
Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann,
Markus Schilhabel, Gernot Gloeckner, Matthias Platzer, and Jurgen Suhnel
6. Comparative Microbial Genome Visualization Using GenomeViz
Rohit Ghai and Trinad Chakraborty
7. BugView: A Tool for Genome Visualization and Comparison
David P. Leader
8. CGAS: Comparative Genome Annotation System
Kwangmin Choi, Youngik Yang, and Sun Kim

Section II-Sequence Alignments

9. BLAST Quick Start: An Example-driven Web-based BLAST Tutorial
David Wheeler and Medha Bhagwat
10. Psi-BLAST Tutorial
Medha Bhagwat, L. Aravind
11. Organizing and Updating Whole Genome BLAST Searches with REHAB
David J. Esteban, Aijazuddin Syed, Chris Upton
12. Alignment of Genomic Sequences Using DIALIGN
Burkhard Morgenstern
13. An Introduction to the Lagan Alignment Toolkit
Michael Brudno
14. Aligning Multiple Whole Genomes with Mercator and Mavid
Colin N. Dewey
15. Mulan: Multiple-Sequence Alignment to Predict Functional Elements
in Genomic Sequences
Gabriela G. Loots and Ivan Ovcharenko
16. Improving Pairwise Sequence Alignment between Distantly Related

Section III-Identification of Conserved Sequences and Biases in Codon

17. Discovering Sequence Motifs
Timothy L. Bailey
18. Discovery of conserved motifs in promoters of orthologous genes in
Rekin's Janky and Jacques van Helden
19. PhyME: A Software Tool for Finding Motifs in Sets of Orthologous
Saurabh Sinha
20. Comparative Genomics-based Orthologous Promoter Analysis using the
DoOP database and the DoOPSearch web tool
Endre Barta
21. Discovery of motifs in promoters of co-regulated genes
Olivier Sand and Jacques van Helden
22. Fastcompare: A non-alignment approach for genome-scale discovery
of DNA and mRNA regulatory elements using network-level conservation
Olivier Elemento and Saeed Tavazoie
23. Phylogenetic footprinting to find functional DNA elements
Austen R. D. Ganley and Takehiko Kobayashi
24. Detecting Regulatory Sites using PhyloGibbs
Rahul Siddharthan and Erik Van Nimwegen
25. Using the Gibbs Motif Sampler for Phylogenetic Footprinting
William Thompson, Sean Conlan, LeeAnn McCue, Charles E. Lawrence
26. Web-based Identification of Evolutionary Conserved DNA
cis-regulatory elements
Panayiotis V. Benos, David L. Corcoran, Eleanor Feingold
27. Exploring conservation of transcription factor binding sites with
Eugene Berezikov, Victor Guryev, Edwin Cuppen
28. Computational and Statistical Methodologies for Orfeome Primary
Structure Analysis
Gabriela Moura, Miguel Pinheiro, Adelaide Valente Freitas, Jose Luis
Oliveira, and Manuel A. S. Santos

Section IV-Identification and Structural Characterization of non-coding

29. Comparative analysis of RNA genes: the caRNAc software
Helene Touzet
30. Efficient annotation of bacterial genomes for small, non-coding
RNAs using the integrative computational tool sRNAPredict2
Jonathan Livny
31. Methods for Multiple Alignment and
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