Computational Biology and Chemistry
Subcellular Localization Prediction with New Protein Encoding Schemes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Subsequence-based feature map for protein function classification
Computational Biology and Chemistry
Prediction of cis/trans isomerization using feature selection and support vector machines
Journal of Biomedical Informatics
Pattern analysis for the prediction of fungal pro-peptide cleavage sites
Discrete Applied Mathematics
Time-sensitive feature mining for temporal sequence classification
PRICAI'10 Proceedings of the 11th Pacific Rim international conference on Trends in artificial intelligence
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Motivation: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. Results: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved ∼81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. Availability:http://staff.vbi.vt.edu/volkan/p2sl and http://www.i-cancer.fen.bilkent.edu.tr/p2sl Contact: rengul@bilkent.edu.tr