Research On Family Of Multiple Sequence Alignment Algorithms Via Components Assembly

In recent years,with the development of high-throughput sequencing technology and the implementation of a series of genome projects,biological information data has exploded,but the data does not represent information.The main purpose of bioinformatics research is to obtain information with biological significance from a large amount of data.Sequence alignment is a basic and important method of comparative genomics,it is based on the chemical basis of biology.Multiple sequence alignment is an important part of sequence alignment research,which is widely used in sequence analysis,sequence annotation,structure and function prediction of genes and proteins,phylogenetic tree analysis and other fields.Multiple sequence alignment algorithm has high specificity and different algorithms are suitable for different research environments.At present,the commonly used multiple sequence alignment is based on the assembly of multiple sub-algorithms under the guidance of bioinformatics theory.However,the existing researches mainly focus on the specific steps of a specific algorithm,and the lack of algorithm framework research with high abstraction of domain level leads to the complexity and redundancy of multiple sequence alignment algorithms.Researchers' selection of sequence alignment algorithms often produces deviation,which will affect the subsequent research.With the development of multiple sequence alignment algorithm,the maintainability and reusability of algorithm software become increasingly significant,which will affect the efficiency of the development of multiple sequence alignment algorithm software.The component-based development method applies the idea of software reuse,which can improve the efficiency,reliability and reduce the cost of software development.The core of software development lies in the development of its internal algorithm.The methodology of software components can also be applied in the development of algorithm,and the algorithm can be further assembled according to the form of component assembly,which greatly improves the development efficiency,reliability and maintainability of the algorithm.Through the research on family of multiple sequence alignment algorithms,it is found that the domain of multiple sequence alignment algorithm(MSAA)includes pairwise sequence alignment algorithm(PSAA),heuristic multiple sequence alignment algorithm(HMSAA),phylogenetic tree algorithm(PTA)and objective function(OF).According to the idea of generative programming,domain feature modeling and interaction design of algorithm components are carried out for MSAA,a multiple sequence alignment algorithm component library is established with the support of PAR.A progressive alignment algorithm based on phylogenetic tree is developed and experiments are carried out to verify the feasibility and superiority of this method.In order to facilitate the assembly operation of algorithm components,an assembly platform of sequence alignment algorithm components based on B/S architecture is established.Users do not need to understand the internal implementation of the algorithm in the platform,and they can generate an executable multiple sequence alignment algorithm by selecting the algorithm components that meet the constraints.