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Evolving Regular Expression-Based Sequence Classifiers for Protein Nuclear Localisation

  • Amine Heddad
  • Markus Brameier
  • Robert M. MacCallum
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3005)

Abstract

A number of bioinformatics tools use regular expression (RE) matching to locate protein or DNA sequence motifs that have been discovered by researchers in the laboratory. For example, patterns representing nuclear localisation signals (NLSs) are used to predict nuclear localisation. NLSs are not yet well understood, and so the set of currently known NLSs may be incomplete. Here we use genetic programming (GP) to generate RE-based classifiers for nuclear localisation. While the approach is a supervised one (with respect to protein location), it is unsupervised with respect to already-known NLSs. It therefore has the potential to discover new NLS motifs. We apply both tree-based and linear GP to the problem. The inclusion of predicted secondary structure in the input does not improve performance. Benchmarking shows that our majority classifiers are competitive with existing tools. The evolved REs are usually “NLS-like” and work is underway to analyse these for novelty.

Keywords

Regular Expression Nucleic Acid Research Linear Genetic Programming Protein Nuclear Localisation Nuclear Localisation Signal Motif 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Amine Heddad
    • 1
  • Markus Brameier
    • 1
  • Robert M. MacCallum
    • 1
  1. 1.Stockholm Bioinformatics Center Stockholm UniversityStockholmSweden

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