TRFolder

TRFolder predicts core structural elements of telomerase RNA (TR) across species, with emphasis on fungal genomes, to enable identification and characterization of TR template region, downstream pseudoknot, boundary element, core-closing stem, and triple helix.

Key Features:

• Core structure prediction: Identifies five fundamental TR substructures: template region, downstream pseudoknot, boundary element, core-closing stem, and triple helix.
• Implementation: Provided as a command-line Python application.
• Species flexibility: Applicable to fungal genomes and extended to predict characteristic TR structures in non-fungal species.
• Detection of complex motifs: Specifically targets complex structures including pseudoknots and triple helices that are critical to TR function.
• Robustness to divergence: Employs techniques to overcome challenges posed by rapid evolutionary divergence of TR sequences.
• Validation and comparative analysis: Used to confirm and refine core structures in Saccharomyces and Kluyveromyces and to predict novel structures in Schizosaccharomyces pombe, Candida albicans, and other yeast species.

Scientific Applications:

• Structural annotation of TRs: Identification and characterization of core TR elements across diverse genomes.
• Comparative and evolutionary analysis: Investigation of TR evolutionary dynamics and divergence across fungal species and beyond.
• Support for experimental studies: Validation and refinement of previously studied TR core structures and generation of novel structural hypotheses for experimental follow-up.

Methodology:

Implemented as a command-line Python application that employs techniques to predict core TR substructures, including pseudoknots and triple helices, and to mitigate challenges from rapid evolutionary divergence.