Pattern matching algorithms are usually used as detecting process in intrusion detection system. The efficiency of these algorithms is affected by the performance of the intrusion detection system which reflects the requirement of a new investigation in this field. Four matching algorithms and a combined of two algorithms, for intrusion detection system based on new DNA encoding, are applied for evaluation of their achievements. These algorithms are Brute-force algorithm, Boyer-Moore algorithm, Horspool algorithm, Knuth-Morris-Pratt algorithm, and the combined of Boyer-Moore algorithm and Knuth–Morris– Pratt algorithm. The performance of the proposed approach is calculated based on the executed time, where these algorithms are applied on NSL-KDD dataset. The obtained results showed that the average time for matching for all NSL-KDD dataset records, based on Brute-force algorithm, Boyer-Moore algorithm, Horspool algorithm, Knuth-Morris-Pratt algorithm, and the combined of Boyer-Moore algorithm and Knuth–Morris–Pratt algorithm are equal to 18.4, 11.5, 9.23, 7.5, and 23.2 seconds respectively. These results demonstrated that using single algorithm achieved better time than combined algorithms, and Knuth-Morris-Pratt algorithm gives the best result than the rest of the other three algorithms. The results are reasonable and acceptable when they are compared with previous systems.