SEQOPTICS: a protein sequence clustering system

Background: Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Ordering Points To Identify the Clustering Structure) is an attractive approach due to its emphasis on visualization of results and support for interactive work, e.g., in choosing parameters. However, OPTICS has not been used, as far as we know, for protein sequence clustering. Results: In this paper, a system of clustering proteins, SEQOPTICS (SEQuence clustering with OPTICS) is demonstrated. The system is implemented with Smith-Waterman as protein distance measurement and OPTICS at its core to perform protein sequence clustering. SEQOPTICS is tested with four data sets from different data sources. Visualization of the sequence clustering structure is demonstrated as well. Conclusion: The system was evaluated by comparison with other existing methods. Analysis of the resul...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Yonghui Chen, Kevin D. Reilly, Alan P. Sprague, Zhijie Guan
• Keywords: BMCBI 2006, Protein, Protein Distance Measurements, Protein Sequence