$re = '/;(?=(?:[^\[\]]*\[[^\[\]]*\])*[^\[\]]*$)
#;|\[|\]/x';
$str = '#first split:
gene1[position1:oldAA-newAA;position2:oldAA-newAA;position3:oldXX-newXX];gene2[position1:oldAA-newAA];gene3[v];gene4;gene5
#second split:
gene1[position1:oldAA-newAA;position2:oldAA-newAA;position3:oldXX-newXX]';
$subst = "";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php