Pyvorin for Computational Biology

Protein Folding Heuristics

Contact map prediction and energy minimisation loops.

def contact_map(sequence, threshold=8.0):
    n = len(sequence)
    contacts = []
    for i in range(n):
        for j in range(i+1, n):
            if distance(i, j) < threshold:
                contacts.append((i, j))
    return contacts

Phylogenetic Trees

UPGMA and neighbour-joining algorithms.

Sequence Assembly

De Bruijn graph traversal and overlap detection.