RNA Structure

RNA secondary structure prediction and alignment.

RNA Folding with ViennaRNA

# Fold single sequence
RNAfold < sequence.fasta > structure.txt

# With constraints
RNAfold -C < sequence.fasta

# Suboptimal structures
RNAsubopt -e 5 < sequence.fasta

Python Interface

import RNA

# Fold sequence
seq = "GGGAAACCCGGGAAACCC"
structure, mfe = RNA.fold(seq)
print(f"Structure: {structure}")
print(f"MFE: {mfe} kcal/mol")

# Partition function
fc = RNA.fold_compound(seq)
structure, mfe = fc.mfe()
fc.pf()

Structural Alignment

# LocARNA for structural alignment
mlocarna sequences.fasta --output output_dir

# Infernal for RNA family alignment
cmscan --tblout results.tbl Rfam.cm query.fasta

Dot-Bracket Notation

def parse_dotbracket(structure):
    """Parse dot-bracket notation."""
    pairs = []
    stack = []
    for i, char in enumerate(structure):
        if char == '(':
            stack.append(i)
        elif char == ')':
            if stack:
                pairs.append((stack.pop(), i))
    return pairs