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Main description:
Comparative Genomics, Volume 2, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume 2 contains the last three of seven sections. In the second volume, the fifth section describes a number of tools for comparative analysis of domain and gene families. These tools are particularly useful for predicting protein function as well as potential protein-protein interactions. In the sixth section, methods for comparing groups of genes and gene order are discussed, as are several tools for analyzing genome evolution. Finally, the seventh section deals with experimental comparative genomics. This section includes methods for comparing gene copy number across an entire genome, comparative genomic hybridization, SNP analysis, as well as genome-wide mapping and typing systems for bacterial genomes. 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 1 is also available from Humana Press.
Feature:
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
Back cover:
Comparative Genomics, Volume 2, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume 2 contains the last three of seven sections. In the second volume, the fifth section describes a number of tools for comparative analysis of domain and gene families. These tools are particularly useful for predicting protein function as well as potential protein-protein interactions. In the sixth section, methods for comparing groups of genes and gene order are discussed, as are several tools for analyzing genome evolution. Finally, the seventh section deals with experimental comparative genomics. This section includes methods for comparing gene copy number across an entire genome, comparative genomic hybridization, SNP analysis, as well as genome-wide mapping and typing systems for bacterial genomes. 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 1 is also available from Humana Press.
Contents:
Comparative Genomics-Volume II
Table of Contents
Section V-Comparative Analysis of Domain and Protein Families
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. StudyingBacterial 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
PRODUCT DETAILS
Publisher: Springer (Humana Press)
Publication date: December, 2011
Pages: 434
Weight: 666g
Availability: Not available (reason unspecified)
Subcategories: Biochemistry, Genetics
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