DOI: 10.1016/s1672-0229(06)60016-8. PredSL: A Tool for the N-Terminal Sequence-Based Prediction of Protein Subcellular Localization

PredSL: A Tool for the N-Terminal Sequence-Based Prediction of Protein Subcellular Localization

10.1016/s1672-0229(06)60016-8

Crossref journal-article

Oxford University Press (OUP)

Genomics, Proteomics & Bioinformatics (286)

Abstract

Abstract The ability to predict the subcellular localization of a protein from its sequence is of great importance, as it provides information about the protein’s function. We present a computational tool, PredSL, which utilizes neural networks, Markov chains, profile hidden Markov models, and scoring matrices for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence. It aims to classify proteins into five groups: chloroplast, thylakoid, mitochondrion, secretory pathway, and “other”. When tested in a five-fold cross-validation procedure, PredSL demonstrates 86.7% and 87.1% overall accuracy for the plant and non-plant datasets, respectively. Compared with TargetP, which is the most widely used method to date, and LumenP, the results of PredSL are comparable in most cases. When tested on the experimentally verified proteins of the Saccharomyces cerevisiae genome, PredSL performs comparably if not better than any available algorithm for the same task. Furthermore, PredSL is the only method capable for the prediction of these subcellular localizations that is available as a stand-alone application through the URL: http://bioinformatics.biol.uoa.gr/PredSL/.

Bibliography

Petsalaki, E. I., Bagos, P. G., Litou, Z. I., & Hamodrakas, S. J. (2006). PredSL: A Tool for the N-Terminal Sequence-Based Prediction of Protein Subcellular Localization. Genomics, Proteomics & Bioinformatics, 4(1), 48â55.

Authors 4

Evangelia I. Petsalaki (first)
Pantelis G. Bagos (additional)
Zoi I. Litou (additional)
Stavros J. Hamodrakas (additional)

References 30 Referenced 125

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{'key': '2024051008221587200_bib2', 'first-page': '291', 'article-title': 'An overview on predicting the subcellular location of a protein', 'volume': '2', 'author': 'Feng', 'year': '2002', 'journal-title': 'In Silico Biol.'} / In Silico Biol. / An overview on predicting the subcellular location of a protein by Feng (2002)
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10.1006/jmbi.2000.3903 / J. Mol. Biol. / Predicting subcellular localization of proteins based on their N-terminal amino acid sequence by Emanuelsson (2000)
10.1002/(SICI)1097-0134(19990101)34:1<137::AID-PROT11>3.0.CO;2-O / Proteins / Prediction of membrane protein types and subcellular locations by Chou (1999)
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10.1093/bioinformatics/btg222 / Bioinformatics / Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs by Park (2003)
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10.1093/bioinformatics/bth171 / Bioinformatics / MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins by Guda (2004)
{'key': '2024051008221587200_bib14', 'first-page': '122', 'article-title': 'Prediction of signal peptides and signal anchors by a hidden Markov model', 'volume': '6', 'author': 'Nielsen', 'year': '1998', 'journal-title': 'Proc. Int. Conf. Intell. Syst. Mol. Biol.'} / Proc. Int. Conf. Intell. Syst. Mol. Biol. / Prediction of signal peptides and signal anchors by a hidden Markov model by Nielsen (1998)
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Dates

Type	When
Created	19 years, 4 months ago (April 19, 2006, 1:45 p.m.)
Deposited	1 year, 3 months ago (May 10, 2024, 4:22 a.m.)
Indexed	2 months, 2 weeks ago (June 9, 2025, 4:44 p.m.)
Issued	19 years, 5 months ago (March 1, 2006)
Published	19 years, 5 months ago (March 1, 2006)
Published Online	19 years, 4 months ago (April 18, 2006)
Published Print	19 years, 5 months ago (March 1, 2006)

Funders 1

thylakoid targeting peptide prediction

BibTeX

@article{Petsalaki_2006, title={PredSL: A Tool for the N-Terminal Sequence-Based Prediction of Protein Subcellular Localization}, volume={4}, ISSN={2210-3244}, url={http://dx.doi.org/10.1016/s1672-0229(06)60016-8}, DOI={10.1016/s1672-0229(06)60016-8}, number={1}, journal={Genomics, Proteomics & Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Petsalaki, Evangelia I. and Bagos, Pantelis G. and Litou, Zoi I. and Hamodrakas, Stavros J.}, year={2006}, month=mar, pages={48–55} }

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  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        3,
        1
      ]
    ]
  },
  "references-count": 30,
  "journal-issue": {
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          1
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      ]
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  },
  "URL": "http://dx.doi.org/10.1016/S1672-0229(06)60016-8",
  "relation": {},
  "ISSN": [
    "1672-0229",
    "2210-3244"
  ],
  "subject": [],
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      [
        2006,
        3
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      [
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        1
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}