Prediction of signal peptides and signal anchors by a hidden Markovmodel

Henrik Nielsen, Anders Stærmose Krogh

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

    Abstract

    A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our data, the length distributions for the three regions are significantly different from expectations. For instance, the assigned hydrophobic region is between 8 and 12 residues long in almost all eukaryotic signal peptides. This analysis also makes obvious the difference between eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. The model can be used to predict the location of the cleavage site, which it finds correctly in nearly 70% of signal peptides in a cross-validated test - almost the same accuracy as the best previous method. One of the problems for existing prediction methods is the poor discrimination between signal peptides and uncleaved signal anchors, but this is substantially improved by the hidden Markov model when expanding it with a very simple signal anchor model.
    Original languageEnglish
    Title of host publicationProceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology
    Place of PublicationMenlo Park
    PublisherAAAI Press
    Publication date1998
    Pages122-130
    Publication statusPublished - 1998
    EventSixth International Conference on Intelligent Systems for Molecular Biology - Montreal, Canada
    Duration: 28 Jun 19981 Jul 1998

    Conference

    ConferenceSixth International Conference on Intelligent Systems for Molecular Biology
    CountryCanada
    CityMontreal
    Period28/06/199801/07/1998

    Cite this

    Nielsen, H., & Krogh, A. S. (1998). Prediction of signal peptides and signal anchors by a hidden Markovmodel. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (pp. 122-130). Menlo Park: AAAI Press.
    Nielsen, Henrik ; Krogh, Anders Stærmose. / Prediction of signal peptides and signal anchors by a hidden Markovmodel. Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Menlo Park : AAAI Press, 1998. pp. 122-130
    @inproceedings{4bd48bafe3db4da197e938ea31a942d6,
    title = "Prediction of signal peptides and signal anchors by a hidden Markovmodel",
    abstract = "A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our data, the length distributions for the three regions are significantly different from expectations. For instance, the assigned hydrophobic region is between 8 and 12 residues long in almost all eukaryotic signal peptides. This analysis also makes obvious the difference between eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. The model can be used to predict the location of the cleavage site, which it finds correctly in nearly 70{\%} of signal peptides in a cross-validated test - almost the same accuracy as the best previous method. One of the problems for existing prediction methods is the poor discrimination between signal peptides and uncleaved signal anchors, but this is substantially improved by the hidden Markov model when expanding it with a very simple signal anchor model.",
    author = "Henrik Nielsen and Krogh, {Anders St{\ae}rmose}",
    year = "1998",
    language = "English",
    pages = "122--130",
    booktitle = "Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology",
    publisher = "AAAI Press",

    }

    Nielsen, H & Krogh, AS 1998, Prediction of signal peptides and signal anchors by a hidden Markovmodel. in Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, pp. 122-130, Sixth International Conference on Intelligent Systems for Molecular Biology, Montreal, Canada, 28/06/1998.

    Prediction of signal peptides and signal anchors by a hidden Markovmodel. / Nielsen, Henrik; Krogh, Anders Stærmose.

    Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Menlo Park : AAAI Press, 1998. p. 122-130.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

    TY - GEN

    T1 - Prediction of signal peptides and signal anchors by a hidden Markovmodel

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    AU - Krogh, Anders Stærmose

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    N2 - A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our data, the length distributions for the three regions are significantly different from expectations. For instance, the assigned hydrophobic region is between 8 and 12 residues long in almost all eukaryotic signal peptides. This analysis also makes obvious the difference between eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. The model can be used to predict the location of the cleavage site, which it finds correctly in nearly 70% of signal peptides in a cross-validated test - almost the same accuracy as the best previous method. One of the problems for existing prediction methods is the poor discrimination between signal peptides and uncleaved signal anchors, but this is substantially improved by the hidden Markov model when expanding it with a very simple signal anchor model.

    AB - A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our data, the length distributions for the three regions are significantly different from expectations. For instance, the assigned hydrophobic region is between 8 and 12 residues long in almost all eukaryotic signal peptides. This analysis also makes obvious the difference between eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. The model can be used to predict the location of the cleavage site, which it finds correctly in nearly 70% of signal peptides in a cross-validated test - almost the same accuracy as the best previous method. One of the problems for existing prediction methods is the poor discrimination between signal peptides and uncleaved signal anchors, but this is substantially improved by the hidden Markov model when expanding it with a very simple signal anchor model.

    M3 - Article in proceedings

    SP - 122

    EP - 130

    BT - Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology

    PB - AAAI Press

    CY - Menlo Park

    ER -

    Nielsen H, Krogh AS. Prediction of signal peptides and signal anchors by a hidden Markovmodel. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Menlo Park: AAAI Press. 1998. p. 122-130