I don't know what "longest common [[chain? substring?]]" has to do with "percent difference", especially after seeing in a comment that you expect a very small % difference between two strings that differ by one character in the middle (so their longest common substring is about one half of the strings' length).
Ignoring the "longest common" strangeness, and defining "percent difference" as the edit distance between the strings divided by the max length (times 100 of course;-), what about:
def levenshtein_distance(first, second):
"""Find the Levenshtein distance between two strings."""
if len(first) > len(second):
first, second = second, first
if len(second) == 0:
return len(first)
first_length = len(first) + 1
second_length = len(second) + 1
distance_matrix = [[0] * second_length for x in range(first_length)]
for i in range(first_length):
distance_matrix[i][0] = i
for j in range(second_length):
distance_matrix[0][j]=j
for i in xrange(1, first_length):
for j in range(1, second_length):
deletion = distance_matrix[i-1][j] + 1
insertion = distance_matrix[i][j-1] + 1
substitution = distance_matrix[i-1][j-1]
if first[i-1] != second[j-1]:
substitution += 1
distance_matrix[i][j] = min(insertion, deletion, substitution)
return distance_matrix[first_length-1][second_length-1]
def percent_diff(first, second):
return 100*levenshtein_distance(a, b) / float(max(len(a), len(b)))
a = "the quick brown fox"
b = "the quick vrown fox"
print '%.2f' % percent_diff(a, b)
The Levenshtein function is from Stavros' blog. The result in this case would be 5.26 (percent difference).