Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
Journal of Computational and Applied Mathematics
Classifying molecular sequences using a linkage graph with their pairwise similarities
Theoretical Computer Science - Special issue: Genome informatics
Indexing large metric spaces for similarity search queries
ACM Transactions on Database Systems (TODS)
Data mining: concepts and techniques
Data mining: concepts and techniques
Knowledge Acquisition Via Incremental Conceptual Clustering
Machine Learning
PLATCOM: a Platform for Computational Comparative Genomics
Bioinformatics
Clustering sequences by overlap
International Journal of Data Mining and Bioinformatics
Performance evaluation of protein sequence clustering tools
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
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In this paper, we first discuss issues in clustering biological sequences with graph properties, which inspired the design of our sequence clustering algorithm BAG. BAG recursively utilises several graph properties: biconnectedness, articulation points, pquasi-completeness, and domain knowledge specific to biological sequence clustering. To reduce the fragmentation issue, we have developed a new metric called cluster utility to guide cluster splitting. Clusters are then merged back with less stringent constraints. Experiments with the entire COG database and other sequence databases show that BAG can cluster a large number of sequences accurately while keeping the number of fragmented clusters significantly low.