RNA Analyzer

RNA Analyzer identifies and characterizes regulatory RNA elements and predicts RNA secondary structure from FASTA-formatted single or batch RNA sequences to support studies of translation, stability, localization, and RNA function.

Key Features:

• Region Identification: Segments RNA molecules into 5' untranslated region (5' UTR), coding sequence (CDS), and 3' untranslated region (3' UTR) for mRNAs.
• Signal Detection: Screens identified regions for polyadenylation sites, AU-rich regions, and other regulatory motifs involved in post-transcriptional regulation.
• RNA Folding Analysis: Performs a rapid folding routine to predict RNA secondary structure.
• Structural Content Evaluation: Assesses structural content including stem-loop formations and overall fold energy.
• Consensus Template Matching: Matches sequences and predicted structures to consensus templates for functional RNAs such as Iron Response Element (IRE), tRNA, and catalytic RNAs (e.g., trans-splicing).
• Batch FASTA Input: Accepts and analyzes single sequences or batches of sequences provided in FASTA format.

Scientific Applications:

• Gene expression regulation: Identification of regions and signals that influence translation, mRNA stability, and subcellular localization.
• Translational control analysis: Detection of functional motifs associated with translational regulation such as the Iron Response Element (IRE).
• Structural and catalytic RNA studies: Prediction of secondary structure and identification of motifs relevant to structural RNAs (e.g., tRNA) and catalytic RNAs involved in processes like trans-splicing.

Methodology:

Segmentation of sequences into 5' UTR, CDS and 3' UTR; screening for polyadenylation sites, AU-rich regions and other regulatory motifs; rapid RNA secondary structure prediction (folding routine); evaluation of stem-loop content and fold energy; and consensus-template matching to IRE, tRNA and catalytic RNA motifs using input sequences in FASTA format.