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DNA splice site sequences clustering method for conservativeness analysis

Progress in Natural Science:Materials International 2009年第4期19卷 511-516页

作者： quanwei zhang, qinke peng, tao xu state key laboratory for manufacturing systems engineering, school of electronic and information engineering, xi’an jiaotong university, xi’an 710049, china [a]state key laboratory for manufacturing systems engineering School of Electronic and Information Engineering Xi’an Jiaotong University Xi’an 710049 China

DNA sequences that are near to splice sites have remarkable conservativeness, and many researchers have contributed to the prediction of splice site. In order to mine the underlying biological knowledge, we analyze the conservativeness of DNA splice site adjacent sequences by clustering. Firstly, we propose a kind of DNA splice site sequences clustering method which is based on DBSCAN, and use four kinds of dissimilarity calculating methods. Then, we analyze the conservative feature of the clustering results and the experimental data set.

关键词： Bioinformatics processing Clustering DBSCAN Splice site

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Identification of a combination of SNPs associated with Graves' disease using swarm intelligence

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Science china(Life Sciences) 2011年第2期54卷 139-145页

作者： WEI Bin peng qinke zhang quanwei LI ChenYao state key laboratory for manufacturing systems engineering and school of electronic and information engineering Xi’an Jiaotong UniversityXi’an 710049China MOE key laboratory for Intelligent Networks and Network Security Xi’an Jiaotong UniversityXi’an 710049China electronic and information school of xi’an jiaotong university Xi’an 710049China

Graves' disease,the production of thyroid-stimulating hormone receptor-stimulating antibodies leading to hyperthyroidism,is one of the most common forms of human autoimmune *** is widely agreed that complex diseases are not controlled simply by an individual gene or DNA variation but by their *** nucleotide polymorphisms(SNPs),which are the most common form of DNA variation,have great potential as a medical diagnostic *** this paper,the P-value is used as a SNP pre-selection criterion,and a wrapper algorithm with binary particle swarm optimization is used to find the rule for discriminating between affected and control *** analyzed the association between combinations of SNPs and Graves' disease by investigating 108 SNPs in 384 cases and 652 *** evaluated our method by differentiating between cases and controls in a five-fold cross validation test,and it achieved a 72.9% prediction accuracy with a combination of 17 *** experimental results showed that SNPs,even those with a high P-value,have a greater effect on Graves' disease when acting in a combination.

关键词： Graves' disease single nucleotide polymorphism case-control study swarm intelligence

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