Comparative Genomics

I Genome Visualization and Annotation.- 1 Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools 3Inna Dubchak 3.- 2 Comparative Genomic Analysis Using the UCSC Genome Browser 17Donna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb Miller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, and W. James Kent 17.- 3 Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System 35Victor M. Markowitz and Nikos C. Kyrpides 35.- 4 WebACT: An Online Genome Comparison Suite 57James C. Abbott, David M. Aanensen, and Stephen D. Bentley 57.- 5 GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy75Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glöckner, Matthias Platzer, and Jürgen Sühnel 75.- 6 Comparative Microbial Genome Visualization Using GenomeViz 97Rohit Ghai and Trinad Chakraborty 97.- 7 BugView: A Tool for Genome Visualization and Comparison 109David P. Leader 109.- 8 CGAS: A Comparative Genome Annotation System133Kwangmin Choi, Youngik Yang, and Sun Kim 133.- II Sequence Alignments.- 9 BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial 149David Wheeler and Medha Bhagwat 149.- 10 PSI-BLAST Tutorial 177Medha Bhagwat and L. Aravind 177.- 11 Organizing and Updating Whole Genome BLAST Searches with ReHAB 187David J. Esteban, Aijazuddin Syed, and Chris Upton 187.- 12 Alignment of Genomic Sequences Using DIALIGN 195Burkhard Morgenstern 195.- 13 An Introduction to the Lagan Alignment Toolkit 205Michael Brudno 205.- 14 Aligning Multiple Whole Genomes with Mercator and MAVID 221Colin N. Dewey 221.- 15 Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences 237Gabriela G. Loots and IvanOvcharenko 237.- 16 Improving Pairwise Sequence Alignment between Distantly Related Proteins 255Jin-an Feng 255.- III Identification of Conserved Sequences and Biases in Codon Usage.- 17 Discovering Sequence Motifs 271Timothy L. Bailey 271.- 18 Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes 293Rekin's Janky and Jacques van Helden 293.- 19 PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences 309Saurabh Sinha 309.- 20 Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool 319Endre Barta 319.- 21 Discovery of Motifs in Promoters of Coregulated Genes 329Olivier Sand and Jacques van Helden 329.- 22 Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation 349Olivier Elemento and Saeed Tavazoie 349.- 23 Phylogenetic Footprinting to Find Functional DNA Elements 367Austen R. D. Ganley and Takehiko Kobayashi 367.- 24 Detecting Regulatory Sites Using PhyloGibbs 381Rahul Siddharthan and Erik van Nimwegen 381.- 25 Using the Gibbs Motif Sampler for Phylogenetic Footprinting 403William Thompson, Sean Conlan, Lee Ann McCue, and Charles E. Lawrence 403.- 26 Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements 425Panayiotis V. Benos, David L. Corcoran, and Eleanor Feingold 425.- 27 Exploring Conservation of Transcription Factor Binding Sites with CONREAL 437Eugene Berezikov, Victor Guryev, and Edwin Cuppen 437.- 28 Computational and Statistical Methodologies for ORFeome Primary Structure Analysis 449Gabriela Moura, Miguel Pinheiro, Adelaide Valente Freitas, José Luís Oliveira, and Manuel A. S. Santos 449.- IV Identification and Structural Characterization of Noncoding RNAs.- 29Comparative Analysis of RNA Genes: The caRNAc Software 465Hélène Touzet 465.- 30 Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2 475Jonathan Livny 475.- 31 Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA 489Sven Siebert and Rolf Backofen 489.- 32 Prediction of Structural Noncoding RNAs With RNAz 503Stefan Washietl 503.- 33 RNA Consensus Structure Prediction With RNAalifold 527Ivo L. Hofacker 527.