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Performance Comparison of Clustering Methods for Gene Family Data

Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 133)

Abstract

Clustering gene sequences into families is important for understanding and predicting gene function. Many clustering algorithms and alignment-free similarity measures have been used to analyze gene family. The clustering results can be influenced by the similarity measure and clustering algorithm used. We compare the results from running four commonly used clustering methods, including K-means, single-linkage clustering, complete-linkage clustering and average-linkage clustering, on three alignment-free similarity measures. We try to find out which method should provide the best clustering result based on real-world gene family datasets. Experiment results show that average-linkage clustering with our similarity measure, DMk, performed best.

Keywords

Gene family Clustering algorithm Similarity Measure 

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Copyright information

© Springer-Verlag GmbH Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Cognitive Science DepartmentXiamen UniversityXiamenChina
  2. 2.Fujian Key Laboratory of the Brain-like Intelligent SystemsXiamen UniversityXiamenChina
  3. 3.Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina

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