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In Silico Tools for Gene Discovery

  • Book
  • © 2011

Overview

Editors:
  1. Bing Yu

    1. Royal Prince Alfred Hospital, Dept. of Molecular & Clinical Genetics, University of Sydney, Camperdown, Australia

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    You can also search for this editor in PubMed   Google Scholar

  2. Marcus Hinchcliffe

    1. Royal Prince Alfred Hospital, Dept. Molecular & Clinical Genetics, University of Sydney, Camperdown, Australia

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Provides brief introductions and clear instructions for the applications of each particular in silico tool
  • Features a wide variety of tools with easy to follow methodologies
  • Includes key tips and vital implementation advice straight from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 760)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Accessing and Selecting Genetic Markers from Available Resources

    • Christopher G. Bell
    Pages 1-17

  3. Linkage Analysis

    • Jennifer H. Barrett, M. Dawn Teare
    Pages 19-33

  4. Association Mapping

    • Jodie N. Painter, Dale R. Nyholt, Grant W. Montgomery
    Pages 35-52

  5. The ForeSee (4C) Approach for Integrative Analysis in Gene Discovery

    • Yike Guo, Robin E.J. Munro, Dimitrios Kalaitzopoulos, Anita Grigoriadis
    Pages 53-71

  6. R Statistical Tools for Gene Discovery

    • Andrea S. Foulkes, Kinman Au
    Pages 73-90

  7. In Silico PCR Analysis

    • Bing Yu, Changbin Zhang
    Pages 91-107

  8. In Silico Analysis of the Exome for Gene Discovery

    • Marcus Hinchcliffe, Paul Webster
    Pages 109-128

  9. In Silico Knowledge and Content Tracking

    • Herman van Haagen, Barend Mons
    Pages 129-140

  10. Application of Gene Ontology to Gene Identification

    • Hugo P. Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria, Francisco M. Couto
    Pages 141-157

  11. Phenotype Mining for Functional Genomics and Gene Discovery

    • Philip Groth, Ulf Leser, Bertram Weiss
    Pages 159-173

  12. Conceptual Thinking for In Silico Prioritization of Candidate Disease Genes

    • Nicki Tiffin
    Pages 175-187

  13. Web Tools for the Prioritization of Candidate Disease Genes

    • Martin Oti, Sara Ballouz, Merridee A. Wouters
    Pages 189-206

  14. Comparative View of In Silico DNA Sequencing Analysis Tools

    • Sissades Tongsima, Anunchai Assawamakin, Jittima Piriyapongsa, Philip J. Shaw
    Pages 207-221

  15. Mutation Surveyor: An In Silico Tool for Sequencing Analysis

    • Chongmei Dong, Bing Yu
    Pages 223-237

  16. In Silico Searching for Disease-Associated Functional DNA Variants

    • Rao Sethumadhavan, C. George Priya Doss, R. Rajasekaran
    Pages 239-250

  17. In Silico Prediction of Transcriptional Factor-Binding Sites

    • Dmitry Y. Oshchepkov, Victor G. Levitsky
    Pages 251-267

  18. In Silico Prediction of Splice-Affecting Nucleotide Variants

    • Claude Houdayer
    Pages 269-281

  19. In Silico Tools for qPCR Assay Design and Data Analysis

    • Stephen Bustin, Anders Bergkvist, Tania Nolan
    Pages 283-306

  20. RNA Structure Prediction

    • Stephan H. Bernhart
    Pages 307-323
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Keywords

About this book

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.

Editors and Affiliations

  • Royal Prince Alfred Hospital, Dept. of Molecular & Clinical Genetics, University of Sydney, Camperdown, Australia

    Bing Yu

  • Royal Prince Alfred Hospital, Dept. Molecular & Clinical Genetics, University of Sydney, Camperdown, Australia

    Marcus Hinchcliffe

Bibliographic Information

  • Book Title: In Silico Tools for Gene Discovery

  • Editors: Bing Yu, Marcus Hinchcliffe

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-176-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-61779-175-8Published: 25 July 2011

  • Softcover ISBN: 978-1-4939-6188-7Published: 23 August 2016

  • eBook ISBN: 978-1-61779-176-5Published: 25 July 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 365

  • Topics: Human Genetics, Gene Function

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