Quadrupia

Quadrupia catalogs G-quadruplex sequences across 108,449 reference genomes, enabling exploration of G-quadruplex structure distribution, taxonomic patterns, and functional genomic positioning across the tree of life.

Key Features:

• Genome-scale G-quadruplex identification: Identifies 140,181,277 G-quadruplexes using regular expressions and G4hunter methods.
• G-quadruplex clustering: Hosts 319,784 clusters of 20 or more members annotated with taxonomic distributions, multiple sequence alignments, profile hidden Markov models, and cross-references to G-quadruplex 3D structures.
• Functional genomic analysis: Examines G-quadruplex orientation and positioning across functional genomic elements in different taxa, including leading strand preference in bacteria with single replication origins.
• Experimental validation: Validates frequently observed G-quadruplexes using CD-spectroscopy, UV melting, and fluorescent-based approaches.

Scientific Applications:

• Evolutionary biology: Facilitates study of how G-quadruplex structures have shaped organismal evolution across the diversity of life.
• Comparative genomics: Enables examination of G-quadruplex distribution patterns and taxonomic differences across 108,449 reference genomes.
• Structural biology: Supports analysis of G-quadruplex 3D structures through clustered sequence alignments and profile hidden Markov models.
• Functional genomics: Investigates preferential orientation and positioning of G-quadruplexes in functional genomic elements such as transcription, replication, and telomere maintenance regions.

Methodology:

G-quadruplex identification employs regular expressions and G4hunter methods. Clusters are annotated with taxonomic distributions, multiple sequence alignments, profile hidden Markov models, and cross-references to G-quadruplex 3D structures. Experimental validation uses CD-spectroscopy, UV melting, and fluorescent-based approaches.