Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework

As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm; some computing errors may occur. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. A star alignment algorithm is designed and generated to demonstrate the development process.

Research on Components Assembly Platform of Biological Sequences Alignment Algorithm

After years of development, the complexity of the biological sequence alignment algorithm is gradually increasing, and the lack of high abstract level domain research leads to the complexity of its algorithm development and improvement. By applying the idea of software components to the design and development of algorithms, the development efficiency and reliability of biological sequence alignment algorithms can be effectively improved. The component assembly platform applies related assembly technology, which simplifies the operation difficulty of component assembly and facilitates the maintenance and optimization of the algorithm. At the same time, a friendly visual interface is used to intuitively complete the assembly of algorithm components, and an executable sequence alignment algorithm program is obtained, which can directly carry out alignment computing.

Traffic Type Recognition Method for Unknown Protocol—Applying Fuzzy Inference

In this paper, we propose a system that can recognize traffic types without prior knowledge of static features such as protocol header information by combining protocol analysis based on an ecological sequence alignment algorithm in a bioinformatics and fuzzy inference system. The algorithm proposed in this paper obtained up to a 91% level of performance at a similar level to several existing algorithms in experiments using datasets containing various types of traffic. In addition, it showed an excellent accuracy of 82.5% or more even under severe conditions that lowered the amount of data to a level of at least 40% or only included data in the middle of the traffic. This shows that the problem of dependence on initial data that frequently occurs in existing machine learning and deep learning-based traffic classification algorithms does not appear in the proposed algorithm. Furthermore, based on the ability to directly extract traffic characteristics without being dependent on static field values, it has secured the ability to respond with a small number of data by taking advantage of the flexibility of the membership function of the fuzzy inference engine. Through this, the applicability to low-power and low-performance environments such as IoT networks was confirmed. In this paper, we describe in detail the theoretical background for constructing such an algorithm and relevant experiments and considerations for actual verification.