AmpliconDesign

AmpliconDesign automates high-throughput PCR primer design, validation, and analysis for bisulfite-treated genomic DNA (BT-DNA) to enable accurate DNA methylation profiling.

Key Features:

• High-Throughput Primer Design: Automates the design of PCR primers for bisulfite-treated DNA to enable scalable primer generation for large studies.
• In Silico Bisulfite Conversion: Uses in silico bisulfite-converted DNA sequences to design primers and validate binding sites specific to BT-DNA.
• Fragmentation Pattern Prediction: Predicts fragmentation patterns for EpiTYPER MassArray to support interpretation of methylation measurements.
• Quality Control Module: Provides computational quality control for assessing and refining primer designs and binding-site specificity.
• ampBS-seq Analysis Workflow: Implements a workflow tailored for deep amplicon bisulfite sequencing (ampBS-seq) to support methylation pattern analysis.

Scientific Applications:

• Epigenetic Biomarker Development: Supports development of epigenetic biomarkers by enabling targeted DNA methylation profiling.
• Targeted DNA Methylation Profiling: Enables targeted analysis of methylation patterns in BT-DNA associated with diseases and biological processes.
• ampBS-seq Studies: Supports deep amplicon bisulfite sequencing (ampBS-seq) experiments for high-resolution methylation analysis.
• EpiTYPER MassArray Analysis: Provides primer design and fragmentation pattern prediction for EpiTYPER MassArray assays.

Methodology:

Computational methods explicitly include in silico bisulfite conversion of reference sequences, automated primer design and binding-site validation using bioinformatics algorithms, fragmentation pattern prediction for EpiTYPER MassArray, and ampBS-seq analysis workflows.