a hybrid distance measure for clustering expressed sequence tags originating from the same gene family聚类的混合距离测量表达序列标签来自相同的基因家族.pdfVIP

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family 1 1 2 Keng-Hoong Ng *, Chin-Kuan Ho , Somnuk Phon-Amnuaisuk 1 Faculty of Computing and Informatics, Multimedia University, Cyberjaya, Malaysia, 2 Faculty of Creative Industries, Universiti Tunku Abdul Rahman, Petaling Jaya, Malaysia Abstract Background: Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster. Recent EST clustering algorithms mostly adopt the alignment-free distance measures, where they tend to yield acceptable clustering accuracies with reasonable computational time. Despite the fact that these clustering methods work satisfactorily on a majority of the EST datasets, they have a common weakness. They are prone to deliver unsatisfactory clustering results when dealing with ESTs from the genes derived from the same family. The root cause is the distance measures applied on them are not sensitive enough to separate these closely related genes. Methodology/Principal Findings: We propose a hybrid distance measure that combines the global and local features extracted from ESTs, with the aim to address the clustering problem faced by ESTs derived from the same gene family. The clustering process is implemented using the DBSCAN algorithm. We test the hybrid distance measure on the ten EST datasets, and the clustering results are compared with the two alignment-free EST clustering tools, i.e. wcd and PEACE. The clustering results indicate that the proposed hybrid distance measure performs relatively better (in terms of clustering accuracy) than b