Sequence-based prediction of protein secretion success in Aspergillus niger

Bastiaan A. Van Den Berg, Jurgen F. Nijkamp, Marcel J.T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos, Dick De Ridder

Research output: Conference contribution

2 Citations (Scopus)

Abstract

The cell-factory Aspergillus niger is widely used for industrial enzyme production. To select potential proteins for large-scale production, we developed a sequence-based classifier that predicts if an over-expressed homologous protein will successfully be produced and secreted. A dataset of 638 proteins was used to train and validate a classifier, using a 10-fold cross-validation protocol. Using a linear discriminant classifier, an average accuracy of 0.85 was achieved. Feature selection results indicate what features are mostly defining for successful protein production, which could be an interesting lead to couple sequence characteristics to biological processes involved in protein production and secretion.

Original languageEnglish
Title of host publicationPattern Recognition in Bioinformatics - 5th IAPR International Conference, PRIB 2010, Proceedings
Pages3-14
Number of pages12
DOIs
Publication statusPublished - 2010
Event5th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2010 - Nijmegen, Netherlands
Duration: szept. 22 2010szept. 24 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6282 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other5th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2010
CountryNetherlands
CityNijmegen
Period9/22/109/24/10

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Van Den Berg, B. A., Nijkamp, J. F., Reinders, M. J. T., Wu, L., Pel, H. J., Roubos, J. A., & De Ridder, D. (2010). Sequence-based prediction of protein secretion success in Aspergillus niger. In Pattern Recognition in Bioinformatics - 5th IAPR International Conference, PRIB 2010, Proceedings (pp. 3-14). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6282 LNBI). https://doi.org/10.1007/978-3-642-16001-1_1