A novel hierarchical clustering algorithm for gene sequences

CORC > 厦门大学 > 软件学院－已发表论文

	A novel hierarchical clustering algorithm for gene sequences
	Wei, Dan ; Jiang, Qingshan ; Wei, Yanjie ; Wang, Shengrui ; Jiang QS(姜青山) ; Wang SR(王声瑞) ; Wei D(魏丹)
刊名	http://dx.doi.org/10.1186/1471-2105-13-174
	2012
关键词	Bioinformatics DNA sequences Functional groups
英文摘要	Background: Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. This method transforms DNA sequences into the feature vectors which contain the occurrence, location and order relation of k-tuples in DNA sequence. Afterwards, a hierarchical procedure is applied to clustering DNA sequences based on the feature vectors.Results: The proposed distance measure and clustering method are evaluated by clustering functionally related genes and by phylogenetic analysis. This method is also compared with BlastClust, CD-HIT-EST and some others. The experimental results show our method is effective in classifying DNA sequences with similar biological characteristics and in discovering the underlying relationship among the sequences.Conclusions: We introduced a novel clustering algorithm which is based on a new sequence similarity measure. It is effective in classifying DNA sequences with similar biological characteristics and in discovering the relationship among the sequences. 漏 2012 Wei et al.; licensee BioMed Central Ltd.
语种	英语
出版者	BioMed Central Ltd.
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/90383]
专题	软件学院－已发表论文
推荐引用方式 GB/T 7714	Wei, Dan,Jiang, Qingshan,Wei, Yanjie,et al. A novel hierarchical clustering algorithm for gene sequences[J]. http://dx.doi.org/10.1186/1471-2105-13-174,2012.
APA	Wei, Dan.,Jiang, Qingshan.,Wei, Yanjie.,Wang, Shengrui.,姜青山.,...&魏丹.(2012).A novel hierarchical clustering algorithm for gene sequences.http://dx.doi.org/10.1186/1471-2105-13-174.
MLA	Wei, Dan,et al."A novel hierarchical clustering algorithm for gene sequences".http://dx.doi.org/10.1186/1471-2105-13-174 (2012).