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The Study of Optimization Algorithm for Multiple Sequence Alignment

Author: YangLi
Tutor: HuoHongWei;LiuZhongWu
School: Xi'an University of Electronic Science and Technology
Course: Software Engineering
Keywords: Global alignment Multiple sequence alignment Progressive algorithm Iterative algorithm Software system Activity Diagram Class diagram
CLC: TP301.6
Type: Master's thesis
Year: 2006
Downloads: 137
Quote: 1
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Abstract


Sequence alignment is an important part in the entire bioinformatics, biomolecular sequence analysis and mining of the foundation. By sequence alignment through sequence than people can be inferred from the DNA sequence of the structure of the protein molecules; through sequence alignment people search to find a new sequence from the gene database; analysis of biological evolution, and one can infer the structure and function of biomolecules Information. This paper first introduces the background knowledge of molecular biology, biological sequence alignment technology introduced, including the basic principles of sequence alignment, global alignment, local alignment, two-sequence comparison and multiple sequence alignment. Several software system for sequence alignment. FASTA search and BLAST search for pairwise sequence alignment to known sequences in the database to identify new sequence. ClustalW program for multiple sequence alignment, it is better a multiple sequence alignment software. In the study of multiple sequence alignment, based progressive algorithm of global multiple sequence alignment algorithm analysis and implementation. Expounded the principle of progressive alignment algorithm, the algorithm used in many of the basic algorithms, dynamic programming algorithm and Needleman-Wunsch algorithm, discussed in the phylogenetic tree construction, as well as close to merging algorithm. Analysis on the impact of the gap penalty points and scoring matrix comparison. On this basis, the object-oriented approach to design a progressive algorithm global multiple sequence alignment software system, the article gives the design idea and UML activity diagrams, UML class diagrams. Software development platform in JBuilderX system and given JBuilderX code automatically generated UML class diagrams. Analysis of the test results by group. In this paper, on the basis of the progressive algorithm can use an iterative algorithm of global multiple sequence than to improve the software system, the paper gives the improved method and the specific design. Finally, the use of 142 BAliBASE database file for testing, the test cases is given. And improved than before and after the results of the comparative analysis, analysis showed that the the iterative method effectively improved incremental algorithm than the system. The content of this paper is progressive algorithm of global multiple sequence alignment of the system by using an iterative algorithm, the system has been improved, experimental testing and analysis, a higher improvement than the effect.

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CLC: > Industrial Technology > Automation technology,computer technology > Computing technology,computer technology > General issues > Theories, methods > Algorithm Theory
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