1. Accessing and Selecting Genetic Markers from Available Resources
Christopher G. Bell
2. Linkage Analysis
Jennifer H. Barrett and M. Dawn Teare
3. Association Mapping
Jodie N. Painter, Dale R. Nyholt, and Grant W. Montgomery
4. The ForeSee (4C) Approach for Integrative Analysis in Gene Discovery
Yike Guo, Robin E.J. Munro, Dimitris Kalaitzopoulos, and Anita Grigoriadis
5. R Statistical Tools for Gene Discovery
Andrea S. Foulkes and Kinman Au
6. In Silico PCR Analysis
Bing Yu and Changbin Zhang
7. In Silico Analysis of the Exome for Gene Discovery
Marcus Hinchcliffe and Paul Webster
8. In Silico Knowledge and Content Tracking
Herman van Haagen and Barend Mons
9. Application of Gene Ontology to Gene Identification
Hugo Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria, and Francisco Couto
10. Phenotype Mining for Functional Genomics and Gene Discovery
Philip Groth, Ulf Leser, and Bertram Weiss
11. Conceptual Thinking for In Silico Prioritization of Candidate Disease Genes
Nicki Tiffin
12. Web Tools for the Prioritization of Candidate Disease Genes
Martin Oti, Sara Ballouz, and Merridee A. Wouters
13. Comparative View of In Silico DNA Sequencing Analysis Tools
Sissades Tongsima, Anunchai Assawamakin, Jittima Piriyapongsa, and Philip J. Shaw
14. Mutation Surveyor: An In Silico Tool for Sequencing Analysis
Chongmei Dong and Bing Yu
15. In Silico Searching for Disease-Associated Functional DNA Variants
Rao Sethumadhavan, C. George Priya Doss, and R. Rajasekaran
16. In Silico Prediction of Transcriptional Factor Binding Sites
Dmitry Y. Oshchepkov and Victor G. Levitsky
17. In Silico Prediction of Splice-Affecting Nucleotide Variants
Claude Houdayer
18. In Silico Tools for qPCR Assay Design and Data Analysis
Stephen Bustin, Anders Bergkvist, and Tania Nolan
19. RNA Structure Prediction
Stephan Bernhart
20. In Silico Prediction of Post-Translational Modifications
Chunmei Liu and Hui Li
21. In Silico Protein Motif Discovery and Structural Analysis
Catherine Mooney,Norman Davey, Alberto J.M. Martin, Ian Walsh, Denis C. Shields, and Gianluca Pollastri
As functional genomics has become one of the major focuses in molecular biology, the need for more sophisticated tools to assist in the identification of the functionality of undefined genes and the correlation of DNA variants with a particular phenotype has increased greatly. In Silico Tools for Gene Discovery collects many common and useful in silico tools available today. The volume begins by investigating locus mapping information on linkage analysis, association mapping, integrative analysis, and exome analysis as well as tools for DNA marker selection, in silico PCR, and statistical analysis. It continues with a section on gene discovery from a defined locus, including gene prioritization, knowledge tracking, and data mining, and concludes with several useful in silico tools presented for the functional characterization of genes, which include DNA sequencing analysis, variant characterization, as well as RNA and protein analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible protocols, and vital notes on troubleshooting and avoiding known pitfalls.
Resourceful and easy to follow,
In Silico Tools for Gene Discovery seeks to facilitate scientists with further key research on locus mapping, to accelerate gene identification, and to help ascertain the functionality of DNA variation.
