rG4-seeker

rG4-seeker identifies and characterizes RNA G-quadruplex (rG4) structures from rG4-seq experiments to enable transcriptome-wide mapping and analysis of canonical and non-canonical rG4 motifs.

Key Features:

• High-Confidence Identification: Identifies novel and non-canonical rG4 structures that are often overlooked by traditional methods.
• Improved False-Positive Discrimination: Reduces false-positive detections through the application of tailored noise models that assess and optimize rG4 calls.
• Enhanced Sensitivity: Leverages knowledge of rG4-seq library preparation chemistry and sequencing data properties to improve detection sensitivity for non-canonical rG4s.
• Replicate-Independent Analysis: Operates independently of replicates to provide consistent results across different datasets.

Scientific Applications:

• Transcriptome-wide rG4 Mapping: Enables genome-scale identification and localization of rG4 structures across transcriptomes using rG4-seq data.
• Non-Canonical rG4 Discovery: Facilitates detection and characterization of non-canonical rG4 motifs that deviate from canonical sequence patterns.
• Sequence-Context Analysis: Supports analysis of the influence of adjacent sequences on rG4 formation and stability.

Methodology:

Connects rG4-seq library preparation chemistry with sequencing data properties; identifies and mitigates indigenous sampling errors and background noise; applies tailored noise models to optimize assessment of rG4 formations.