Performance evaluation of protein sequence clustering tools

  • Authors:

  • Haifeng Liu;Loo-Nin Teow

  • Affiliations:

  • DSO National Laboratories (Kent Ridge), Singapore;DSO National Laboratories (Kent Ridge), Singapore

  • Venue:
  • ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
  • Year:
  • 2005

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Abstract

This paper aims to evaluate the clustering quality of various protein clustering tools that are publicly available as standalone applications. We first review the current protein sequence clustering methods, and introduce a new incrementally clustering tool denoted as PINC. We then propose an intuitive performance metric for evaluating them. The evaluation results of the tools on the public database Pfam are reported.