Hi All, For coding-non coding RNA identification (using Machine learning classifier), I would like to add features extracted from RNA secondary structure. I used RNAfold to get the secondary structure from primary sequence (as dot-bracket representation). Now I want to identify loops, stems, bulges, etc.., from the structure and represent as a feature vector (with some numerical values).
- Is there any tool for this purpose?
- how can I identify the structural elements from dot-bracket notation?
- Is there any better numerical/vector representation for RNA secondary structure for machine learning applications?