QuadFinder

QuadFinder identifies and analyzes nucleotide sequences capable of forming G-quadruplex structures in RNA to investigate their structural properties and potential regulatory roles in gene expression.

Key Features:

• G-quadruplex detection: Detects sequences that form stacked sets of four guanine bases (G-quadruplexes) stabilized by Hoogsteen hydrogen bonding.
• RNA focus: Targets analysis of RNA and unimolecular quadruplex-forming nucleotide sequences.
• Motif variant support: Supports definition and analysis of different variants of the G-quadruplex motif.
• Sequence-context recognition: Identifies G-quadruplex occurrences in genomic contexts, including repetitive DNA regions such as telomeres.
• Prediction and analysis: Performs sequence-based prediction and comprehensive bioinformatics analysis of quadruplex-forming sequences.

Scientific Applications:

• Gene expression regulation: Assess potential regulatory roles of G-quadruplexes influencing gene expression at diverse genomic locations.
• Therapeutic target identification: Identify candidate G-quadruplexes in RNA for exploration as novel therapeutic targets.
• Structural characterization: Study structural properties of G-quadruplexes formed by stacked guanine tetrads and Hoogsteen hydrogen bonding.
• Genomic distribution analysis: Explore distribution and prevalence of quadruplex structures across genomic regions, including telomeric repeats.

Methodology:

Performs sequence-based prediction and comprehensive bioinformatics analyses of unimolecular G-quadruplex-forming nucleotide sequences and supports definition of G-quadruplex motif variants.