Soft Computing

, Volume 15, Issue 8, pp 1631–1642

Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm

  • Ka-Chun Wong
  • Chengbin Peng
  • Man-Hon Wong
  • Kwong-Sak Leung
Original Paper

DOI: 10.1007/s00500-011-0692-5

Cite this article as:
Wong, K., Peng, C., Wong, M. et al. Soft Comput (2011) 15: 1631. doi:10.1007/s00500-011-0692-5

Abstract

Protein-DNA bindings are essential activities. Understanding them forms the basis for further deciphering of biological and genetic systems. In particular, the protein-DNA bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) play a central role in gene transcription. Comprehensive TF-TFBS binding sequence pairs have been found in a recent study. However, they are in one-to-one mappings which cannot fully reflect the many-to-many mappings within the bindings. An evolutionary algorithm is proposed to learn generalized representations (many-to-many mappings) from the TF-TFBS binding sequence pairs (one-to-one mappings). The generalized pairs are shown to be more meaningful than the original TF-TFBS binding sequence pairs. Some representative examples have been analyzed in this study. In particular, it shows that the TF-TFBS binding sequence pairs are not presumably in one-to-one mappings. They can also exhibit many-to-many mappings. The proposed method can help us extract such many-to-many information from the one-to-one TF-TFBS binding sequence pairs found in the previous study, providing further knowledge in understanding the bindings between TFs and TFBSs.

Keywords

BioinformaticsSequenceProteinDNACrowdingGene transcriptionTRANSFACPDB

Supplementary material

500_2011_692_MOESM1_ESM.pdf (1.3 mb)
Supplementary material (PDF 1.32 mb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Ka-Chun Wong
    • 1
    • 2
  • Chengbin Peng
    • 2
  • Man-Hon Wong
    • 1
  • Kwong-Sak Leung
    • 1
  1. 1.Department of Computer Science and EngineeringThe Chinese University of Hong KongShatinHong Kong
  2. 2.Mathematical and Computer Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyJeddahKingdom of Saudi Arabia