TRIPBASE

TRIPBASE curates genome-wide predictions of human genomic DNA and long non-coding RNA (lncRNA) triplexes to improve in-silico identification of RNA–DNA:DNA triple-helical interactions by integrating ASO-mediated capture assay data and Triplexator-based analyses.

Key Features:

• Genome-wide lncRNA triplex predictions: Provides genome-wide predictions of RNA–DNA:DNA triplex binding potential specific to human lncRNAs.
• ASO-mediated capture assay integration: Incorporates experimental evidence from antisense oligonucleotide (ASO)-mediated capture assays to empirically support triplex sites.
• Triplexator-based prediction: Leverages Triplexator and the Hoogsteen base-pairing rule to generate initial RNA–DNA:DNA triplex predictions.
• Six computational attribute filters: Implements six computational attributes proposed as filters to reduce false positives in in-silico triplex prediction.
• Cis-regulatory region annotation: Maps predicted triplexes to cis-regulatory regions of the human genome for genomic-context interpretation.

Scientific Applications:

• Gene regulation studies: Identification of lncRNA-mediated triplexes in cis-regulatory regions to investigate mechanisms of transcriptional regulation.
• Experimental prioritization: Prioritization of computationally predicted triplex sites for experimental validation using ASO capture or related assays.
• Method benchmarking and improvement: Providing empirical data and filter criteria to benchmark, validate, and refine Triplexator-based triplex prediction algorithms.

Methodology:

Integrates ASO-mediated capture assay experimental data with Triplexator-derived predictions and applies six computational attribute filters to refine RNA–DNA:DNA triplex prediction and reduce false positives.