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Frequent subsequence-based protein localization

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Extracellular plant proteins are involved in numerous processes including nutrient acquisition, communication with other soil organisms, protection from pathogens, and resistance to disease and toxic metals. Insofar as these proteins are strategically positioned to play a role in resistance to environmental stress, biologists are interested in proteomic tools in analyzing extracellular proteins. In this paper, we present three methods using frequent subsequences of amino acids: one based on support vector machines (SVM), one based on boosting and FSP, a new frequent subsequence pattern method. We test our methods on a plant dataset and the experimental results show that our methods perform better than the existing approaches based on amino acid composition. © Springer-Verlag Berlin Heidelberg 2006.




Zaïane, O. R., Wang, Y., Goebel, R., & Taylor, G. (2006). Frequent subsequence-based protein localization. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 3916 LNBI, pp. 35–47). Springer Verlag.

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