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, J. Roubos, Dick De Ridder

Research output: Chapter in Book/Report/Conference proceedingConference 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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages3-14
Number of pages12
Volume6282 LNBI
DOIs
Publication statusPublished - 2010
Event5th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2010 - Nijmegen, Netherlands
Duration: Sep 22 2010Sep 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)03029743
ISSN (Electronic)16113349

Other

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

Fingerprint

Aspergillus
Secretion
Proteins
Protein
Prediction
Classifiers
Classifier
Discriminant
Cross-validation
Feature Selection
Industrial plants
Feature extraction
Enzymes
Fold
Predict
Cell

Keywords

  • Aspergillus niger
  • classification
  • protein secretion
  • sequence-based prediction

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Van Den Berg, B. A., Nijkamp, J. F., Reinders, M. J. T., Wu, L., Pel, H. J., Roubos, J., & De Ridder, D. (2010). Sequence-based prediction of protein secretion success in Aspergillus niger. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6282 LNBI, 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

Sequence-based prediction of protein secretion success in Aspergillus niger. / Van Den Berg, Bastiaan A.; Nijkamp, Jurgen F.; Reinders, Marcel J T; Wu, Liang; Pel, Herman J.; Roubos, J.; De Ridder, Dick.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6282 LNBI 2010. p. 3-14 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6282 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Van Den Berg, BA, Nijkamp, JF, Reinders, MJT, Wu, L, Pel, HJ, Roubos, J & De Ridder, D 2010, Sequence-based prediction of protein secretion success in Aspergillus niger. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 6282 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6282 LNBI, pp. 3-14, 5th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2010, Nijmegen, Netherlands, 9/22/10. https://doi.org/10.1007/978-3-642-16001-1_1
Van Den Berg BA, Nijkamp JF, Reinders MJT, Wu L, Pel HJ, Roubos J et al. Sequence-based prediction of protein secretion success in Aspergillus niger. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6282 LNBI. 2010. p. 3-14. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-16001-1_1
Van Den Berg, Bastiaan A. ; Nijkamp, Jurgen F. ; Reinders, Marcel J T ; Wu, Liang ; Pel, Herman J. ; Roubos, J. ; De Ridder, Dick. / Sequence-based prediction of protein secretion success in Aspergillus niger. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6282 LNBI 2010. pp. 3-14 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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