In Silico Tools for Gene Discovery

This volume provides brief introductions and clear instructions for the applications of many common and useful in silico tools. It features a variety of tools with easy to follow methodologies and includes key tips and vital implementation advice.

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.

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

Inhalt

Accessing and Selecting Genetic Markers from Available Resources.- Linkage Analysis.- Association Mapping.- The ForeSee (4C) Approach for Integrative Analysis in Gene Discovery.- R Statistical Tools for Gene Discovery.- In Silico PCR Analysis.- In Silico Analysis of the Exome for Gene Discovery.- In Silico Knowledge and Content Tracking.- Application of Gene Ontology to Gene Identification.- Phenotype Mining for Functional Genomics and Gene Discovery.- Conceptual Thinking for In Silico Prioritization of Candidate Disease Genes.- Web Tools for the Prioritization of Candidate Disease Genes.- Comparative View of In Silico DNA Sequencing Analysis Tools.- Mutation Surveyor: An In Silico Tool for Sequencing Analysis.- In Silico Searching for Disease-Associated Functional DNA Variants.- In Silico Prediction of Transcriptional Factor Binding Sites.- In Silico Prediction of Splice-Affecting Nucleotide Variants.- In Silico Tools for qPCR Assay Design and Data Analysis.- RNA Structure Prediction.- In Silico Prediction of Post-Translational Modifications.- In Silico Protein Motif Discovery and Structural Analysis.