Research On Sequence Alignment Algorithms Based On Network Protocol Reverse

Although the open protocol reverse application has achieved ideal results,it is time-consuming to rely too much on manual analysis.It is of great practical significance to study how to improve the automation and accuracy of protocol reverse.The method of inferring network protocol only depends on the data of network protocol,whether it is to classify the message roughly first,then to align the location format,or to align the sequence first and then to locate the message format finely,is inseparable from the sequence alignment algorithm,so this paper will focus on the reverse sequence alignment algorithm of network protocol as the main research direction.In this paper,the substitution matrix and target function used to measure the alignment results are experimented.Based on the experiment,the influence of the selection of substitution matrix parameters on the alignment results is analyzed clearly.Three commonly used double sequence alignment algorithms,LCS algorithm,NW algorithm and SW algorithm,are compared in time complexity.It is concluded that although the theoretical time complexity of the three algorithms is the same,there are differences in time consumption due to the slight differences in implementation.In order to solve two problems found in the experiment of sequence alignment: there may be multiple correct solutions in the double sequence alignment algorithm,and traversing all the correct solutions will take unpredictable time;in the progressive alignment algorithm,the sequence of alignment will affect the results of alignment.In order to reverse network protocol,sequence alignment results must be accurate.Therefore,this paper designs a sequence alignment algorithm for reverse network protocol,which combines local alignment algorithm and greedy algorithm.Experiments show that the algorithm can obtain correct results without traversing the results,and the sequence selection of alignment sequence will not be correct when using progressive alignment method.The time efficiency of the algorithm is also higher than that of the NW algorithm.