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Comparative Genomics: Volume 2 2007 ed. [Hardback]

  • Formāts: Hardback, 434 pages, height x width: 229x152 mm, weight: 846 g, 1 Illustrations, color; 150 Illustrations, black and white; XVIII, 434 p. 151 illus., 1 illus. in color., 1 Hardback
  • Sērija : Methods in Molecular Biology 396
  • Izdošanas datums: 29-Nov-2007
  • Izdevniecība: Humana Press Inc.
  • ISBN-10: 1934115371
  • ISBN-13: 9781934115374
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  • Formāts: Hardback, 434 pages, height x width: 229x152 mm, weight: 846 g, 1 Illustrations, color; 150 Illustrations, black and white; XVIII, 434 p. 151 illus., 1 illus. in color., 1 Hardback
  • Sērija : Methods in Molecular Biology 396
  • Izdošanas datums: 29-Nov-2007
  • Izdevniecība: Humana Press Inc.
  • ISBN-10: 1934115371
  • ISBN-13: 9781934115374
Citas grāmatas par šo tēmu:
This second volume contains the final three of seven sections of tutorials for molecular biologists who are beginning to use comparative genomic analysis tools in a number of different areas. They consider tools for the comparative analysis of domain and gene families; using groups of genes and gene order to analyze genomic evolution; and experimental comparative genomics dealing with such matters as comparing gene copy number across an entire genome, and genome-wide mapping and typing systems for bacterial genomes. Annotation ©2008 Book News, Inc., Portland, OR (booknews.com)

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.

This volume 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. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel.
Preface v
Contributors xi
Table of Contents---Volume 1
xv
PART I: COMPARATIVE ANALYSIS OF DOMAIN AND PROTEIN FAMILIES
Computational Prediction of Domain Interactions
3(14)
Philipp Pagel
Normann Strack
Matthias Oesterheld
Volker Stumpflen
Dmitrij Frishman
Domain Team: Synteny of Domains is a New Approach in Comparative Genomics
17(14)
Sophie Pasek
Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method
31(12)
Karsten Suhre
Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes
43(16)
Jaina Mistry
Robert Finn
InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison
59(12)
Nicola Mulder
Rolf Apweiler
Gene Annotation and Pathway Mapping in KEGG
71(24)
Kiyoko F. Aoki-Kinoshita
Minoru Kanehisa
PART II: ORTHOLOGS, SYNTENY, AND GENOME EVOLUTION
Ortholog Detection Using the Reciprocal Smallest Distance Algorithm
95(16)
Dennis P. Wall
Todd DeLuca
Finding Conserved Gene Order Across Multiple Genomes
111(10)
Giulio Pavesi
Graziano Pesole
Analysis of Genome Rearrangement by Block-Interchanges
121(14)
Chin Lung Lu
Ying Chih Lin
Yen Lin Huang
Chuan Yi Tang
Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System
135(18)
Aaron E. Darling
Todd J. Treangen
Xavier Messeguer
Nicole T. Perna
Visualization of Syntenic Relationships With SynBrowse
153(12)
Volker Brendel
Stefan Kurtz
Xioakang Pan
Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes
165(20)
Thomas Schmidt
Jens Stoye
PART III: EXPERIMENTAL ANALYSIS OF WHOLE GENOMES: ANALYSIS OF COPY NUMBER AND SEQUENCE POLYMORPHISMS
Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software
185(22)
Seishi Ogawa
Yasuhito Nanya
Go Yamamoto
Oligonucleotide Array Comparative Genomic Hybridization
207(16)
Paul van den Ijssel
Bauke Ylstra
Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization
223(32)
Eduardo N. Taboada
Christian C. Luebbert
John H. E. Nash
DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite
255(12)
Joel Greshock
Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms
267(14)
Brian W. Brunelle
Tracy L. Nicholson
High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity
281(14)
Honghua Li
Hui-Yun Wang
Xiangfeng Cui
Minjie Luo
Guohong Hu
Danielle M. Greenawalt
Irina V. Tereshchenko
James Y. Li
Yi Chu
Richeng Gao
Single Nucleotide Polymorphism Mapping Array Assay
295(20)
Xiaofeng Zhou
David T. W. Wong
Molecular Inversion Probe Assay
315(16)
Farnaz Absalan
Mostafa Ronaghi
novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects
331(14)
Peter De Rijk
Jurgen Del-Favero
Rapid Identification of Single Nucleotide Substitutions Using SeqDoC
345(14)
Mark L. Crowe
SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms
359(12)
Tianhua Niu
Identification of Disease Genes: Example-Driven Web-Based Tutorial
371(24)
Medha Bhagwat
Variable Number Tandem Repeat Typing of Bacteria
395(12)
Siamak P. Yazdankhah
Bjørn-Arne Lindstedt
Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species
407(12)
Meeta Desai
FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping
419(14)
Knud Nairz
Peder Zipperlen
Manuel Schneider
Index 433(112)
Preface ix
Contributors xi
PART 1: GENOME VISUALIZATION AND ANNOTATION
1(146)
Comparative Analysis and Visualization of Genomic Sequences Using Vista Browser and Associated Computational Tools
3(14)
Inna Dubchak
Comparative Genomic Analysis Using the UCSC Genome Browser
17(18)
Donna Karolchik
Gill Bejerano
Angie S. Hinrichs
Robert M. Kuhn
Webb Miller
Kate R. Rosenbloom
Ann S. Zweig
David Haussler
W. James Kent
Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System
35(22)
Victor M. Markowitz
Nikos C. Kyrpides
WebAct: An Online Genome Comparison Suite
57(18)
James C. Abbott
David M. Aanensen
Stephen D. Bentley
GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy
75(22)
Alessandro Romualdi
Marius Felder
Dominic Rose
Ulrike Gausmann
Markus Schilhabel
Gernot Glockner
Matthias Platzer
Jurgen Suhnel
Comparative Microbial Genome Visualization Using GenomeViz
97(12)
Rohit Ghai
Trinad Chakraborty
BugView: A Tool for Genome Visualization and Comparison
109(24)
David P. Leader
CGAS: A Comparative Genome Annotation System
133(14)
Kwangmin Choi
Youngik Yang
Sun Kim
PART 2: SEQUENCE ALIGNMENTS
147(122)
Blast QuickStart: Example-Driven Web-Based Blast Tutorial
149(28)
David Wheeler
Medha Bhagwat
PSI-Blast Tutorial
177(10)
Medha Bhagwat
L. Aravind
Organizing and Updating Whole Genome Blast Searches With ReHAB
187(8)
David J. Esteban
Aijazuddin Syed
Chris Upton
Alignment of Genomic Sequences Using Dialign
195(10)
Burkhard Morgenstern
An Introduction to the Lagan Alignment Toolkit
205(16)
Michael Brudno
Aligning Multiple Whole Genomes with Mercator and Mavid
221(16)
Colin N. Dewey
Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences
237(18)
Gabriela G. Loots
Ivan Ovcharenko
Improving Pairwise Sequence Alignment between Distantly Related Proteins
255(14)
Jin-an Feng
PART 3: IDENTIFICATION OF CONSERVED SEQUENCES AND BIASES IN CODON USAGE
269(194)
Discovering Sequence Motifs
271(22)
Timothy L. Bailey
Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes
293(16)
Rekin's Janky
Jacques van Helden
PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences
309(10)
Saurabh Sinha
Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool
319(10)
Endre Barta
Discovery of Motifs in Promoters of Coregulated Genes
329(20)
Olivier Sand
Jacques van Helden
Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation
349(18)
Olivier Elemento
Saeed Tavazoie
Phylogenetic Footprinting to Find Functional DNA Elements
367(14)
Austen R. D. Ganley
Takehiko Kobayashi
Detecting Regulatory Sites Using PhyloGibbs
381(22)
Rahul Siddharthan
Erik van Nimwegen
Using the Gibbs Motif Sampler for Phylogenetic Footprinting
403(22)
William Thompson
Sean Conlan
Lee Ann McCue
Charles E. Lawrence
Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements
425(12)
Panayiotis V. Benos
David L. Corcoran
Eleanor Feingold
Exploring Conservation of Transcription Factor Binding Sites with Conreal
437(12)
Eugene Berezikov
Victor Guryev
Edwin Cuppen
Computational and Statistical Methodologies for ORFeome Primary Structure Analysis
449(14)
Gabriela Moura
Miguel Pinheiro
Adelaide Valente Freitas
Jose Luis Oliveira
Manuel A. S. Santos
PART 4: IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF NONCODING RNAs
463(82)
Comparative Analysis of RNA Genes: The caRNAc Software
465(10)
Helene Touzet
Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2
475(14)
Jonathan Livny
Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA
489(14)
Sven Siebert
Rolf Backofen
Prediction of Structural Noncoding RNAs With RNAz
503(24)
Stefan Washietl
RNA Consensus Structure Prediction With RNAalifold
527(18)
Ivo L. Hofacker
Index 545