Soft Computing

, Volume 15, Issue 8, pp 1631–1642 | Cite as

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

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


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.


Bioinformatics Sequence Protein DNA Crowding Gene transcription TRANSFAC PDB 



The authors are grateful to the anonymous reviewers for their valuable comments. They would like to thank Tak-Ming Chan for his help on surveying the related works. This research is partially supported by the grants from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project Nos. 414107 and 414708).

Supplementary material

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


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Ka-Chun Wong
    • 1
    • 2
    Email author
  • 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

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