Clustering of Expressed Sequence Tag Using Global and Local Features: A Performance Study

Abstract

Clustering of expressed sequence tag (EST) plays an important role in gene analysis. Alignment-based sequence comparison is commonly used to measure the similarity between sequences, and recently some of the alignment-free comparisons have been introduced. In this paper, we evaluate the role of global and local features extracted from the alignment free approaches i.e., the compression-based method and the generalized relative entropy method. The evaluation is done from the perspective of EST clustering quality. Our evaluation shows that the local feature of EST yields much better clustering quality compared to the global feature. Furthermore, we verified our best clustering result achieved in the experiments with another EST clustering algorithm, wcd, and it shows that our performance is comparable to the later