Re^5: fuzzy match: trim sequences outside of the forward and reverse primer set.

Not much. I though perl package will behave in perl-ish way returning matched part of the string as well as storing somewhere "before-string" and "after-string". What remains is to implement the fuzzy-matching yourself.

If this fuzzy matching would be defined by number of differences between strings then maybe Text::Levenshtein is of use? I mean iterating in simple

for (0..length($str)-$len_of_match)
{
  if(Text::Levenshtein::distance(substr($str, $_, $len_of_match), matc
+hstring) <= $differences_limit)
     { $found = true; last }
}
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