FORCAST

FORCAST facilitates design and evaluation of guide RNAs (gRNAs), genotyping assays, and allele design quality assurance for Cas-mediated genome editing experiments in model organisms.

Key Features:

• Integration of existing tools: Integrates JBrowse, Primer3, BLAST, bwa, and Silica to support guide selection, sequence mapping, assay design, and sequence analysis.
• Guide RNA selection and off-target evaluation: Selects and evaluates gRNAs with prediction and assessment of potential off-target effects to improve editing specificity.
• Genotyping assay design: Designs genotyping assays using Primer3 and BLAST for allele confirmation and validation.
• Allele design quality assurance: Performs quality assurance on allele designs to assess and optimize mutagenesis outcomes.
• Data visualization and storage: Visualizes and catalogs gRNAs and associated experimental parameters for experimental planning and record keeping.

Scientific Applications:

• Cas-mediated genome editing experiment design: Design and evaluation of gRNAs and genotyping assays for mutagenesis in model organisms.
• Off-target risk assessment: Prediction and assessment of off-target effects to reduce unintended genomic modifications.
• Allele design and validation: Optimization and validation of allele constructs and genotyping strategies for mutant generation.
• Sequence mapping and homology searches: Use of BLAST and bwa for sequence mapping and homology assessment relevant to guide selection and assay design.

Methodology:

Integrates JBrowse, Primer3, BLAST, bwa, and Silica into a computational pipeline that performs gRNA selection and optimization, off-target prediction, genotyping assay design, allele design quality assurance, and visualization and storage of experimental data.