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Fast subcellular localization by cascaded fusion of signal-based and homology-based methods

Author(s): Mak, M-W; Wang, W; Kung, Sun-Yuan

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Abstract: Background: The functions of proteins are closely related to their subcellular locations. In the post-genomics era, the amount of gene and protein data grows exponentially, which necessitates the prediction of subcellular localization by computational means.Results: This paper proposes mitigating the computation burden of alignment-based approaches to subcellular localization prediction by a cascaded fusion of cleavage site prediction and profile alignment. Specifically, the informative segments of protein sequences are identified by a cleavage site predictor using the information in their N-terminal shorting signals. Then, the sequences are truncated at the cleavage site positions, and the shortened sequences are passed to PSI-BLAST for computing their profiles. Subcellular localization are subsequently predicted by a profile-to-profile alignment support-vector-machine (SVM) classifier. To further reduce the training and recognition time of the classifier, the SVM classifier is replaced by a new kernel method based on the perturbational discriminant analysis (PDA).Conclusions: Experimental results on a new dataset based on Swiss-Prot Release 57.5 show that the method can make use of the best property of signal- and homology-based approaches and can attain an accuracy comparable to that achieved by using full-length sequences. Analysis of profile-alignment score matrices suggest that both profile creation time and profile alignment time can be reduced without significant reduction in subcellular localization accuracy. It was found that PDA enjoys a short training time as compared to the conventional SVM. We advocate that the method will be important for biologists to conduct large-scale protein annotation or for bioinformaticians to perform preliminary investigations on new algorithms that involve pairwise alignments.
Publication Date: 14-Oct-2011
Electronic Publication Date: 14-Oct-2011
Citation: Mak, M-W, Wang, W, Kung, S-Y. (2011). Fast subcellular localization by cascaded fusion of signal-based and homology-based methods. Proteome Science, 9 (10.1186/1477-5956-9-S1-S8
DOI: doi:10.1186/1477-5956-9-S1-S8
Type of Material: Journal Article
Journal/Proceeding Title: Proteome Science
Version: Final published version. Article is made available in OAR by the publisher's permission or policy.

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