Wong, Ka-ChunKa-ChunWongPeng, ChengbinChengbinPengWong, Man-HonMan-HonWongProf. LEUNG Kwong Sak2023-03-232023-03-232011Soft Computing, 2011, vol. 15 ( 8) , pp. 1631 - 16421432-76431433-7479http://hdl.handle.net/20.500.11861/7533Protein-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. © 2011 Springer-VerlagenBioinformaticsSequenceProteinDNACrowdingGene TranscriptionTRANSFACPDBPeer Reviewed Journal Article10.1007/s00500-011-0692-5