Multiple sequence alignment （MSA） is the alignment among more than two molecular biological sequences, which is a fundamental method to analyze evolutionary events such as mutations, insertions, deletions, and re-ar...Multiple sequence alignment （MSA） is the alignment among more than two molecular biological sequences, which is a fundamental method to analyze evolutionary events such as mutations, insertions, deletions, and re-arrangements. In theory, a dynamic programming algorithm can be employed to produce the optimal MSA. However, this leads to an explosive increase in computing time and memory consumption as the number of sequences increases （Taylor, 1990）. So far, MSA is still regarded as one of the most challenging problems in bioinformatics and computational biology （Chatzou et al., 2016）.展开更多
In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their...In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. In bioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performance cluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the original algorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm (Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.展开更多
A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections...A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections. The approach combines traditional cell formation techniques with sequence alignment algorithms. Firstly, a sequence analysis based cell formation procedure is adopted; then the operation sequences for parts are aligned to maximize machines adjacency in hyperedge representations; finally a tree-shape planar flowline will be obtained for each part family. With the help of a sample of operation sequences obtained from industry, this algorithm is illustrated.展开更多
基金supported by the National Key R&D Program of China (Nos. 2017YFB0202600, 2016YFC1302500, 2016YFB0200400 and 2017YFB0202104)the National Natural Science Foundation of China (Nos. 61772543, U1435222, 61625202, 61272056 and 61771331)Guangdong Provincial Department of Science and Technology (No. 2016B090918122)
文摘Multiple sequence alignment （MSA） is the alignment among more than two molecular biological sequences, which is a fundamental method to analyze evolutionary events such as mutations, insertions, deletions, and re-arrangements. In theory, a dynamic programming algorithm can be employed to produce the optimal MSA. However, this leads to an explosive increase in computing time and memory consumption as the number of sequences increases （Taylor, 1990）. So far, MSA is still regarded as one of the most challenging problems in bioinformatics and computational biology （Chatzou et al., 2016）.
文摘In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. In bioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performance cluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the original algorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm (Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.
文摘A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections. The approach combines traditional cell formation techniques with sequence alignment algorithms. Firstly, a sequence analysis based cell formation procedure is adopted; then the operation sequences for parts are aligned to maximize machines adjacency in hyperedge representations; finally a tree-shape planar flowline will be obtained for each part family. With the help of a sample of operation sequences obtained from industry, this algorithm is illustrated.
