Comparative Genomics : Volume 2 /
| Corporate Author: | |
|---|---|
| Other Authors: | |
| Format: | eBook |
| Language: | English |
| Published: |
Totowa, NJ :
Humana Press : Imprint: Humana,
2007.
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| Edition: | 1st ed. 2007. |
| Series: | Methods in Molecular Biology,
396 |
| Subjects: |
Table of Contents:
- Preface v
- Contributors xi
- Table of Contents-Volume 1 xv
- I: Comparative Analysis of Domain and Protein Families
- 1 Computational Prediction of Domain Interactions 3Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman 3
- 2 Domain Team: Synteny of Domains is a New Approach in Comparative Genomics 17Sophie Pasek 17
- 3 Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method 31Karsten Suhre 31
- 4 Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes 43Jaina Mistry and Robert Finn 43
- 5 InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison 59Nicola Mulder and Rolf Apweiler 59
- 6 Gene Annotation and Pathway Mapping in KEGG 71Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa 71
- II:Orthologs, Synteny, and Genome Evolution
- 7 Ortholog Detection Using the Reciprocal Smallest Distance Algorithm 95Dennis P. Wall and Todd DeLuca 95
- 8 Finding Conserved Gene Order Across Multiple Genomes 111Giulio Pavesi and Graziano Pesole 111
- 9 Analysis of Genome Rearrangement by Block-Interchanges 121Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang 121
- 10 Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System 135Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T. Perna 135
- 11 Visualization of Syntenic Relationships With SynBrowse 153Volker Brendel, Stefan Kurtz, and Xioakang Pan 153
- 12 Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes 165Thomas Schmidt and Jens Stoye 165
- III:Experimental Analysis of Whole Genomes: A NALYSIS OF C OPY N UMBER AND S EQUENCE P OLYMORPHISMS
- 13 Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software 185Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto 185
- 14 Oligonucleotide Array Comparative Genomic Hybridization 207Paul van den IJssel and Bauke Ylstra 207
- 15 Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization 223Eduardo N. Taboada, Christian C. Luebbert, and John H. E. Nash 223
- 16 DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite 255Joel Greshock 255
- 17 Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms 267Brian W. Brunelle and Tracy L. Nicholson 267
- 18 High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity 281Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu, Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and Richeng Gao 281
- 19 Single Nucleotide Polymorphism Mapping Array Assay 295Xiaofeng Zhou and David T. W. Wong 295
- 20 Molecular Inversion Probe Assay 315Farnaz Absalan and Mostafa Ronaghi 315
- 21 novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects 331Peter De Rijk and Jurgen Del-Favero 331
- 22 Rapid Identification of Single Nucleotide Substitutions Using SeqDoC 345Mark L. Crowe 345
- 23 SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms 359Tianhua Niu 359
- 24 Identification of Disease Genes: Example-Driven Web-Based Tutorial 371Medha Bhagwat 371
- 25 Variable Number Tandem Repeat Typing of Bacteria 395Siamak P. Yazdankhah and BjØrn-Arne Lindstedt 395
- 26 Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species 405Meeta Desai 407
- 27 FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping 419Knud Nairz, Peder Zipperlen, and Manuel Schneider 419
- Index 433.