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 easy Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glöckner, Matthias Platzer, and Jürgen Sühnel 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 Proteins Jin-anFeng Section III-Identification of Conserved Sequences and Biases in Codon Usage 17. Discovering Sequence Motifs Timothy L. Bailey 18. Discovery of conserved motifs in promoters of orthologous genes in prokaryotes Rekin's Janky and Jacques van Helden 19. PhyME: A Software Tool for Finding Motifs in Sets of Orthologous Sequences 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 CONREAL 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 RNAs 29. Comparative analysis of RNA genes: the caRNAc software Hélène 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
