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.
Volume 1
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-an Feng
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 Consensus Structure Prediction
of RNAs Implemented in MARNA
Sven Siebert and Rolf Backofen
32. Prediction of structural noncoding RNAs with RNAz
Stefan Washietl
33. RNA Consensus Structure Prediction with RNAalifold
Ivo L. Hofacker
Table of contents
Comparative Genomics-Volume II
Table of Contents
Section V-Comparative Analysis of Domain and Protein Families
Volume 2
1. Computational Prediction of Domain Interactions
Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen,
and Dmitrij Frishman
2. DomainTeam: Synteny of domains is a new approach in comparative
genomics
Sophie Pasek
3. Inference of gene function based on gene fusion events: the Rosetta
Stone method
Karsten Suhre
4. Pfam: A domain-centric method for analyzing proteins and proteomes
Jaina Mistry and Robert Finn
5. InterPro and InterProScan-Tools for Protein Sequence Classification
and Comparison
Nicola Mulder and Rolf Apweiler
6. Gene Annotation and Pathway Mapping in KEGG
Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa
Section VI-Orthologs, Synteny, and Genome Evolution
7. Ortholog Detection using the Smallest Distance Algorithm
Dennis P. Wall and Todd DeLuca
8. Finding Conserved Gene Order Across Multiple Genomes
Giulio Pavesi and Graziano Pesole
9. Analysis of Genome Rearrangement by Block-Interchanges
Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang
10. Analyzing Patterns of microbial evolution using the Mauve Genome
Alignment System
Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T.
Perna
11. Visualization of syntenic relationships with SynBrowse
Volker Brendel, Stefan Kurtz, and Xiaohang Pan
12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detection
in Prokaryotic Genomes
Thomas Schmidt and Jens Stoye
Section VII-Experimental Analysis of Whole Genomes-Analysis of Copy
Number and Sequence Polymorphisms
13. Genome-wide copy number analysis on GeneChip platform using CNAG
2.0 software
Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto
14. Oligonucleotide array comparative genomic hybridization
Paul van den IJssel and Bauke Ylstra
15. Studying Bacterial Genome Dynamics Using Microarray-Based
Comparative Genomic Hybridization
Eduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash
16. CGH analysis using the CGHAnalyzer
Joel Greshock
17. Microarray-based Approach for Genome-Wide Survey of Nucleotide
Polymorphisms
Brian W. Brunelle and Tracy L. Nicholson
18. High-Throughput Genotyping of Single Nucleotide Polymorphisms with
High Sensitivity
Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu,
Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and
Richeng Gao
19. Single nucleotide polymorphism (SNP) mapping array assay
Xiaofeng Zhou and David T. W. Wong
20. Molecular Inversion Probe Assays
Farnaz Absalan and Mostafa Ronaghi
21. novoSNP: variant detection and sequence annotation in resequencing
projects
Peter De Rijk and Jurgen Del-Favero
22. Rapid Identification of Single Nucleotide Substitutions Using
SeqDoc
Mark L. Crowe
23. SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing
Single Nucleotide Polymorphisms
Tianhua Niu
24. Identification of Disease Genes: An Example-driven Web-based
Tutorial
Medha Bhagwat
25. Variable number tandem repeat typing of bacteria
Siamak P. Yazdankhah and Bjørn-Arne Lindstedt
26. Fluorescent amplified fragment length polymorphism (FAFLP)
genotyping of bacterial species
Meeta Desai
27. FLP-mapping: A universal, cost-effective, and automatable method
for gene mapping
Knud Nairz, Peder Zipperlen, and Manuel Schneider