Riboswitch finder

Sequence and structure-based identification of riboswitch motifs

Riboswitch Finder detects riboswitch RNA motifs within mRNA sequences by combining sequence pattern analysis and secondary structure evaluation. Originally developed for high-sensitivity riboswitch variants in Bacillus subtilis, it supports identification of regulatory metabolic binding domains across diverse RNA sequences.

Key Features:

• RNA Motif and Structural Pattern Detection: Identifies conserved riboswitch sequence elements and characteristic secondary structures, including variants described in Bacillus subtilis.
• Secondary Structure Energy Calculation: Computes RNA folding energies to assess structural stability of candidate riboswitches.
• Integrated Sequence–Structure Testing: Applies combined sequence and structural criteria to improve detection sensitivity and specificity.
• Batch FASTA Processing: Analyzes multiple RNA sequences simultaneously for large-scale screening.

Scientific Applications:

• Regulatory RNA and Comparative Genomics Studies: Enables identification and comparative analysis of riboswitch elements to investigate gene regulation and evolutionary conservation.

Methodology:

Riboswitch Finder scans RNA sequences for conserved riboswitch motifs, predicts secondary structures and folding energies, and integrates sequence and structural tests to classify candidate riboswitch elements.