Provides a collection of robust protocols for molecular biologists studying comparative genomics
Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique
A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently
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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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.
Comparative Genomics-Volume ITable of ContentsSection I-Genome Visualization and Annotation1. Comparative analysis and visualization of genomic sequences usingVISTA Browser and associated computational toolsInna Dubchak2. Comparative Genomic Analysis Using the UCSC Genome BrowserDonna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, WebbMiller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent3. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) SystemVictor M. Markowitz and Nikos C. Kyrpides4. WebACT: An Online Genome Comparison SuiteJames C. Abbott, David M. Aanensen, and Stephen D. Bentley5. GenColors: Annotation and Comparative Genomics of Prokaryotes madeeasyAlessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann,Markus Schilhabel, Gernot Glöckner, Matthias Platzer, and Jürgen Sühnel6. Comparative Microbial Genome Visualization Using GenomeVizRohit Ghai and Trinad Chakraborty7. BugView: A Tool for Genome Visualization and ComparisonDavid P. Leader8. CGAS: Comparative Genome Annotation SystemKwangmin Choi, Youngik Yang, and Sun KimSection II-Sequence Alignments9. BLAST Quick Start: An Example-driven Web-based BLAST TutorialDavid Wheeler and Medha Bhagwat10. Psi-BLAST TutorialMedha Bhagwat, L. Aravind11. Organizing and Updating Whole Genome BLAST Searches with REHABDavid J. Esteban, Aijazuddin Syed, Chris Upton12. Alignment of Genomic Sequences Using DIALIGNBurkhard Morgenstern13. An Introduction to the Lagan Alignment ToolkitMichael Brudno14. Aligning Multiple Whole Genomes with Mercator and MavidColin N. Dewey15. Mulan: Multiple-Sequence Alignment to Predict Functional Elementsin Genomic SequencesGabriela G. Loots and Ivan Ovcharenko16. Improving Pairwise Sequence Alignment between Distantly RelatedProteinsJin-anFengSection III-Identification of Conserved Sequences and Biases in CodonUsage17. Discovering Sequence MotifsTimothy L. Bailey18. Discovery of conserved motifs in promoters of orthologous genes inprokaryotesRekin's Janky and Jacques van Helden19. PhyME: A Software Tool for Finding Motifs in Sets of OrthologousSequencesSaurabh Sinha20. Comparative Genomics-based Orthologous Promoter Analysis using theDoOP database and the DoOPSearch web toolEndre Barta21. Discovery of motifs in promoters of co-regulated genesOlivier Sand and Jacques van Helden22. Fastcompare: A non-alignment approach for genome-scale discoveryof DNA and mRNA regulatory elements using network-level conservationOlivier Elemento and Saeed Tavazoie23. Phylogenetic footprinting to find functional DNA elementsAusten R. D. Ganley and Takehiko Kobayashi24. Detecting Regulatory Sites using PhyloGibbsRahul Siddharthan and Erik Van Nimwegen25. Using the Gibbs Motif Sampler for Phylogenetic FootprintingWilliam Thompson, Sean Conlan, LeeAnn McCue, Charles E. Lawrence26. Web-based Identification of Evolutionary Conserved DNAcis-regulatory elementsPanayiotis V. Benos, David L. Corcoran, Eleanor Feingold27. Exploring conservation of tranillegalscription factor binding sites withCONREALEugene Berezikov, Victor Guryev, Edwin Cuppen28. Computational and Statistical Methodologies for Orfeome PrimaryStructure AnalysisGabriela Moura, Miguel Pinheiro, Adelaide Valente Freitas, Jose LuisOliveira, and Manuel A. S. SantosSection IV-Identification and Structural Characterization of non-codingRNAs29. Comparative analysis of RNA genes: the caRNAc softwareHélène Touzet30. Efficient annotation of bacterial genomes for small, non-codingRNAs using the integrative computational tool sRNAPredict2Jonathan Livny31. Methods for Multiple Alignment and
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.
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 Tranillegalscription 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.
Inhaltsverzeichnis
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 tranillegalscription 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
Klappentext
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.
Provides a collection of robust protocols for molecular biologists studying comparative genomics
Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique
A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently
