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    <p>If I understand correctly:</p> <p>1) Start with ATG</p> <p>2) A number of triplets, except 'TAG', 'TAA', and 'TGA'</p> <p>3) One of the triplets 'TAG', 'TAA', or 'TGA'</p> <p>This should work:</p> <pre><code>/ (ATG) # Step 1 ((?!TAG|TAA|TGA)[ACGT]{3})+ # Step 2 (TAG|TAA|TGA) # Step 3 /x </code></pre> <p>The difference from you second idea it to move the negative look-ahead inside the quantifier to get 'a number of triplet' step ensuring that neither of the triplets are one of the exceptions</p> <p>This solution does not assume any commonality between the elements in step 2 and step 3. A simpler, but in your case equivalent, formulations would be:</p> <p>1) Match 'ATG'</p> <p>2) Match a number of triplets</p> <p>3) ... until you match 'TAG', 'TAA', 'TGA'.</p> <p>To do this you just need to make the quantifier in step 2 non-greedy, as this would test is Step 3 matches before trying if step 2 matched again.</p> <p>Then the solution would look like:</p> <pre><code>/ (ATG) ([ACGT]{3})*? (TAG|TAA|TGA) /x </code></pre> <p>An alternative interpretation might be:</p> <p>1) Start with ATG</p> <p>2) A number of triplets</p> <p>3) One of the triplets 'TAG', 'TAA', 'TGA'</p> <p>4) The substring found in step 2 must not contain the substrings 'TAG', 'TAA', 'TGA'.</p> <p>In this case I would solve it using two regular expressions. On implementing step 1-3 and one for the test in step 4:</p> <pre><code> $sequence =~ /(ATG)([ACGT]{3})(TAG|TAA|TGA)/ and $2 !~ /TAG|TAA|TGA/; </code></pre>
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    1. POHow to exclude a specific pattern from regex in perl?
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    1. COThat won't work, since you've included `[ACGT]` in the negative lookahead. See here: http://rubular.com/r/ISc65tpRez
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      1. USAsad Saeeduddin
    2. CO@Asad: Adding the final `$` makes it work.
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    3. CONo I didn't. The negative look-ahead is `(?!TAG|TAA|TGA)`
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