PLEXY

PLEXY predicts thermodynamically optimal interactions between box C/D small nucleolar RNAs (snoRNAs) and candidate target RNA sequences to identify putative target sites implicated in 2'-O-ribose methylation, rRNA maturation, and splicing regulation.

Key Features:

• Thermodynamic interaction computation: Computes thermodynamically optimal interactions between box C/D snoRNAs and target RNAs.
• Dynamic programming algorithm: Uses a dynamic programming algorithm to evaluate possible binding configurations.
• Energetic evaluation: Identifies energetically favorable duplexes by assessing binding configurations.
• Duplex structure filtering: Applies filters on duplex structures to refine predictions.
• Large-scale sequence scanning: Scans large input sequences efficiently to support high-throughput analyses.
• Orphan snoRNA target prediction: Predicts targets of 'orphan' box C/D snoRNAs to support functional hypotheses.

Scientific Applications:

• Box C/D snoRNA target identification: Predicts putative target sites of box C/D snoRNAs across candidate RNA sequences.
• 2'-O-ribose methylation studies: Supports investigation of snoRNA-mediated 2'-O-ribose methylation by identifying interacting targets.
• rRNA maturation research: Facilitates identification of snoRNA interactions relevant to rRNA maturation.
• Splicing regulation analysis: Enables exploration of snoRNA roles in splicing regulation of certain mRNAs via predicted interactions.
• High-throughput target discovery: Enables large-scale scanning to generate candidate target lists for downstream validation.

Methodology:

Computes thermodynamically optimal snoRNA–target duplexes using a dynamic programming algorithm that evaluates binding configurations, scans large input sequences, and applies filters on duplex structures to identify energetically favorable interactions.