Ribo-ODDR

Ribo-ODDR: Computational design of rRNA-depleting oligonucleotides for Ribo-seq

Ribo-ODDR designs biotinylated oligos to enhance ribosomal RNA (rRNA) depletion in ribosome profiling (Ribo-seq) experiments. It analyzes pilot sequencing data and known rRNA sequences to identify abundant rRNA fragments and selects complementary oligonucleotides optimized for condition-specific depletion.

Key Features:

• Custom Oligo Design: Identifies abundant rRNA fragments from pilot Ribo-seq data and designs complementary biotinylated oligos targeting condition-specific rRNA fragment profiles.
• Depleting Potential Calculation: Quantifies the predicted efficiency of each candidate oligo in depleting rRNA fragments.
• User-Defined Filtering: Selects oligos based on configurable criteria to meet experimental constraints.
• Multi-Format Output: Exports oligo sequences and annotations in FASTA, BED, GFF, and CSV formats, with optional off-target information in TXT format.

Scientific Applications:

• Ribo-seq Library Optimization: Increases sequencing depth and data quality by reducing rRNA-derived reads, enabling improved analysis of translated RNAs at nucleotide resolution.

Methodology:

Ribo-ODDR maps pilot Ribo-seq reads to reference rRNA sequences to identify high-abundance rRNA fragments. It generates complementary biotinylated oligonucleotides, computes their depleting potential based on fragment coverage, and ranks candidates according to user-defined selection parameters.