We all know (or should), that the g option in regular expressions doesn't actually give you "all occurrences" of a substring in a string. For example:

perl -wle '$_="ababa";(@matches) = /aba/g; print @matches;'

prints "aba" only once, even though there are TWO occurences of "aba" in the original string.

I'm faced with a similar situation. I'm trying to scan a string of DNA for ALL occurrences of /..g.{18}c/. For any given (random) sequence, there is about a 6% chance of matching the above substring. However, when used like the following:

my @string_var = $DNA_sequence =~ /..g.{18}c/ig;

then we only get 1/2 of the predicted amount. This is entirely due to the fact that given the substring length/composition, there is a very good chance that two matching patterns overlap (like in the "ababa" example).

So here's the question: How do I get around this so that I can match the missing substrings? Can it be done with a regexp, or substr, or is there a module that can help?

In reply to regexp g option: finds all occurrences? ha!! by cyphedude

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