BAG: a graph theoretic sequence clustering algorithm.

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.