In Silico Tools for Gene Discovery

ISBN-13: 9781617791758 / Angielski / Twarda / 2011 / 365 str.

Bing Yu; Marcus Hinchcliffe

Opis

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.

Spis treści

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