ElTetrado

ElTetrado identifies and classifies tetrads and quadruplexes in nucleic acid 3D structures to analyze secondary-structure topology of canonical and non-canonical quadruplex motifs relevant to telomeres and transcriptional regulatory regions.

Key Features:

• Identification: Detects tetrads and quadruplexes by analyzing base-pairing patterns in DNA and RNA 3D structures.
• Classification (ONZ taxonomy): Classifies tetrads and quadruplexes according to the ONZ taxonomy based on secondary-structure topology.
• Secondary-structure topology analysis: Uses secondary-structure topology to distinguish between different structural configurations of tetrads and quadruplexes.
• Support for canonical and non-canonical motifs: Accommodates both canonical and non-canonical quadruplex motifs.
• Notation and visualization outputs: Generates dot-bracket notation and graphical depictions that reflect the unique secondary-structure topology of identified quadruplexes.

Scientific Applications:

• Telomere studies: Characterizes tetrads and quadruplexes present in telomeric regions.
• Transcriptional regulation: Analyzes quadruplex motifs in transcriptional regulatory regions to support studies of gene regulation.
• Non-canonical motif characterization: Enables analysis of non-canonical quadruplexes beyond canonical sequence-focused approaches.
• Complementary structural analysis: Provides secondary-structure topology insights that complement sequence and 3D structural examinations.

Methodology:

Analyzes base-pairing patterns in DNA/RNA 3D structures to identify tetrads and quadruplexes, classifies motifs using secondary-structure topology according to the ONZ taxonomy, and outputs dot-bracket notation and graphical depictions.