Because mining complete set of frequent patterns from dense database could be impractical, an interesting alternative has been proposed recently. Instead of mining the complete set of frequent patterns, the new model ...Because mining complete set of frequent patterns from dense database could be impractical, an interesting alternative has been proposed recently. Instead of mining the complete set of frequent patterns, the new model only finds out the maximal frequent patterns, which can generate all frequent patterns. FP-growth algorithm is one of the most efficient frequent-pattern mining methods published so far. However, because FP-tree and conditional FP-trees must be two-way traversable, a great deal memory is needed in process of mining. This paper proposes an efficient algorithm Unid_FP-Max for mining maximal frequent patterns based on unidirectional FP-tree. Because of generation method of unidirectional FP-tree and conditional unidirectional FP-trees, the algorithm reduces the space consumption to the fullest extent. With the development of two techniques: single path pruning and header table pruning which can cut down many conditional unidirectional FP-trees generated recursively in mining process, Unid_FP-Max further lowers the expense of time and space.展开更多
Phi29 DNA polymerase(Phi29 Pol)has emerged as a powerful tool in the third-generation sequencing technology such as DNA nanoball-based sequencing.However,natural Phi29 Pol with low amplification activity under high-sa...Phi29 DNA polymerase(Phi29 Pol)has emerged as a powerful tool in the third-generation sequencing technology such as DNA nanoball-based sequencing.However,natural Phi29 Pol with low amplification activity under high-salt conditions needs to be engineered to meet specific sequencing demands,which are usually achieved through a time-consuming and iterative trial-and-error process.Herein,we develop a high-throughput screening methodology for efficiently detecting Phi29 Pol mutants with high rolling-circle amplification(RCA)efficiency under high-salt conditions.The method uses a nucleic acid gel stain sensitive to oligonucleotides to achieve the input conversion from enzymatic amplification efficiency to fluorescence intensity in micron-sized droplets.We further demonstrate the potential of this methodology in the first high-throughput droplet sorting of Phi29 Pol.The RCA efficiency of sorted mutant S6 is 1.39-fold that of initial enzyme M2 in 300 mM KCl.Overall,this study provides a cost-effective and rapid solution for improving the performance of Phi29 Pol under high-salt conditions.展开更多
基金Supported by the National Natural Science Foundation of China ( No.60474022)Henan Innovation Project for University Prominent Research Talents (No.2007KYCX018)
文摘Because mining complete set of frequent patterns from dense database could be impractical, an interesting alternative has been proposed recently. Instead of mining the complete set of frequent patterns, the new model only finds out the maximal frequent patterns, which can generate all frequent patterns. FP-growth algorithm is one of the most efficient frequent-pattern mining methods published so far. However, because FP-tree and conditional FP-trees must be two-way traversable, a great deal memory is needed in process of mining. This paper proposes an efficient algorithm Unid_FP-Max for mining maximal frequent patterns based on unidirectional FP-tree. Because of generation method of unidirectional FP-tree and conditional unidirectional FP-trees, the algorithm reduces the space consumption to the fullest extent. With the development of two techniques: single path pruning and header table pruning which can cut down many conditional unidirectional FP-trees generated recursively in mining process, Unid_FP-Max further lowers the expense of time and space.
基金supported by the National Key Research and Development Program of China(2022YFC3401303)Shandong Province Key R&D Program(Major Science and Technology Innovation Project)Project(2023CXGC010714)+1 种基金Natural Science Foundation of Jiangsu Province(BK20240202)Key Technological Project of Jiangxi Province(20244AFH82001)。
文摘Phi29 DNA polymerase(Phi29 Pol)has emerged as a powerful tool in the third-generation sequencing technology such as DNA nanoball-based sequencing.However,natural Phi29 Pol with low amplification activity under high-salt conditions needs to be engineered to meet specific sequencing demands,which are usually achieved through a time-consuming and iterative trial-and-error process.Herein,we develop a high-throughput screening methodology for efficiently detecting Phi29 Pol mutants with high rolling-circle amplification(RCA)efficiency under high-salt conditions.The method uses a nucleic acid gel stain sensitive to oligonucleotides to achieve the input conversion from enzymatic amplification efficiency to fluorescence intensity in micron-sized droplets.We further demonstrate the potential of this methodology in the first high-throughput droplet sorting of Phi29 Pol.The RCA efficiency of sorted mutant S6 is 1.39-fold that of initial enzyme M2 in 300 mM KCl.Overall,this study provides a cost-effective and rapid solution for improving the performance of Phi29 Pol under high-salt conditions.
