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

Zien, A; Ong, CS

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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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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0013-D23D-1 Version Permalink: https://hdl.handle.net/21.11116/0000-0002-87F9-D

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Creators:
Zien, A^{1, 2}, Author
Ong, CS^{1, 2, 3}, Author

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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: Date issued: 2006-04

Publication Status: Issued

Pages: 18

Publishing info: Tübingen, Germany : Max Planck Institute for Biological Cybernetics

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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: -