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Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition”
May-June 2012 (vol. 9 no. 3)
pp. 940-941
Denise Fagundes-Lima, Federal University of Ouro Preto, Ouro Preto
Gerald Weber, Federal University of Minas Gerais, Belo Horizonte
We comment on the flexibility profiles calculated by Zeng et al., and show that these profiles do not represent the local flexibility of the DNA molecule. If one takes into account the physics of elasticity, the averaged flexibility profile show an additional peak which is missed in the original calculation. We show that it is not possible to calculate the flexibility of a 6-mer using tetranucleotide elastic constants, the shortest sequence is a 7-mer. For 6-mers, dinucleotide or trinucleotide parameters are needed. We present calculations for dinucleotide flexibility parameters and show that the same additional peak is present for both 7--mers and 6-mers.

[1] J. Zeng, X.-Y. Zhao, X.-Q. Cao, and H. Yan, "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 3, pp. 550-562, July-Sept. 2010.
[2] M.J. Packer, M.P. Dauncey, and C.A. Hunter, "Sequence-Dependent DNA Structure: Tetranucleotide Conformational Maps," J. Molecular Biology, vol. 295, no. 1, pp. 85-103, 2000.
[3] R. Yamashita, Y. Suzuki, H. Wakaguri, K. Tsuritani, K. Nakai, and S. Sugano, "DBTSS: Database of Human Transcription Start Sites, Progress Report 2006," Nucleic Acids Research, vol. 34, no. suppl 1, pp. D86-D89, 2006.
[4] G. Weber, J.W. Essex, and C. Neylon, "Probing the Microscopic Flexibility of DNA from Melting Temperatures," Nature Physics, vol. 5, pp. 769-773, 2009.

Index Terms:
Promoter analysis, DNA elasticity, flexibility profiles.
Denise Fagundes-Lima, Gerald Weber, "Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition”," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 3, pp. 940-941, May-June 2012, doi:10.1109/TCBB.2011.130
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