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  An Automated Combination of Sequence Motif Kernels for Predicting Protein Subcellular Localization

Zien, A., & Ong, C.(2006). An Automated Combination of Sequence Motif Kernels for Predicting Protein Subcellular Localization (146). Tübingen, Germany: Max Planck Institute for Biological Cybernetics.

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MPIK-TR-146.pdf (Publisher version), 212KB
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 Creators:
Zien, A1, 2, Author              
Ong, CS1, 2, 3, Author              
Affiliations:
1Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
2Max Planck Institute for Biological Cybernetics, Max Planck Society, Spemannstrasse 38, 72076 Tübingen, DE, ou_1497794              
3Friedrich Miescher Laboratory, Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, DE, ou_2575692              

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 Abstract: Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions. While many predictive computational tools have been proposed, they tend to have complicated architectures and require many design decisions from the developer. We propose an elegant and fully automated approach to building a prediction system for protein subcellular localization. We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We further propose a multiclass support vector machine method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we generalize our method to optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets.

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 Dates: 2006-04
 Publication Status: Published in print
 Pages: 18
 Publishing info: Tübingen, Germany : Max Planck Institute for Biological Cybernetics
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 Rev. Type: -
 Identifiers: Report Nr.: 146
BibTex Citekey: 3943
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Title: Technical Report of the Max Planck Institute for Biological Cybernetics
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Pages: - Volume / Issue: 146 Sequence Number: - Start / End Page: - Identifier: -