AnthOligo

AnthOligo automates generation of oligonucleotide sequences for capture and enrichment of large and complex genomic regions using region-specific extraction (RSE) targeting long DNA fragments (15–20 kb) for magnetic bead–based capture following enzymatic extension of hybridized oligonucleotides.

Key Features:

• Automated Oligo Sequence Generation: Generates oligonucleotide candidates and optimizes melting temperature (Tm), Gibbs free energy (ΔG), and minimizes primer-dimer formation for pooled experiments.
• Customizable Parameters and Input: Accepts target region input in BED format and allows customization of selection criteria for oligo design.
• RSE Probe Design: Tailors probes for region-specific extraction (RSE) compatible with enzymatic extension of hybridized oligonucleotides and magnetic bead capture of 15–20 kb fragments.
• Applications to Gene Panels and CGH: Designs internal oligos for gene panel analysis and probes for comparative genomic hybridization (CGH) arrays.
• Validation: Demonstrated capture of the Major Histocompatibility Complex (MHC) in experimental testing.

Scientific Applications:

• Targeted Genomic Resequencing: Supports design of capture probes for targeted resequencing of large genomic regions.
• Gene Panel Analysis: Enables creation of internal oligos for targeted gene panels.
• Comparative Genomic Hybridization (CGH): Generates probes suitable for large-scale CGH array experiments.

Methodology:

Given a BED file of target regions, AnthOligo computes oligonucleotide candidates and evaluates melting temperature (Tm), Gibbs free energy (ΔG), and primer-dimer formation to select probes suitable for capture.