AptCompare

AptCompare performs de novo motif discovery in RNA aptamers from high-throughput sequencing (HTS) SELEX experiments to identify and prioritize candidate high-affinity ligands.

Key Features:

• Integration of analytical algorithms: Integrates six widely recognized motif-detection algorithms for RNA aptamer analysis.
• Weighted ranking system: Applies a weighted ranking system to prioritize candidate aptamers based on consensus among the integrated algorithms.
• SELEX HTS data processing: Processes high-throughput sequencing (HTS) data from multiple rounds of SELEX to capture enrichment dynamics.
• Consensus-ranked reads: Produces a consensus-ranked list of sequencing reads to narrow down potential aptamer candidates.
• Experimental validation correlation: Provides sequence rankings that have been validated to correlate with experimental binding affinities by bench assays.

Scientific Applications:

• De novo motif discovery: Identification of enriched sequence motifs in RNA aptamer pools derived from SELEX HTS data.
• Candidate prioritization for binding studies: Prioritization of aptamer sequences for follow-up binding assays based on consensus rankings and enrichment across SELEX rounds.
• Identification of high-affinity ligands: Selection of candidate RNA aptamers as potential therapeutic or diagnostic ligands through predicted enrichment and ranking.

Methodology:

Processes HTS data from multiple SELEX rounds using an integrated suite of six motif-detection algorithms and computes a weighted consensus ranking of sequencing reads.