How it works

Each input DNA sequence is processed in the following way. The window of specified length (default 147, which is the length of DNA in a nucleosome) is slid along the input sequence, and nucleosome-exclusion sequences within the window are counted. The length of the window can be changed. We consider three classes of rigid DNA sequences:

1. A_n, n ³ 10 (poly-A)

2. T_n, n ³ 10 (poly-T)

3. (C/G)₃-N₂-(C/G)₃-N₂-(C/G)₃

Predictions of nucleosome positioning depend on exclusion sequences clustering in the input DNA sequence. Depending on which output format is chosen, NXSensor will highlight either exclusion sequences (option “Exclusion sequences”) or segments of the input DNA sequence where nucleosomes are likely to be (option “Nucleosome segments”).

Related papers

M. Ganapathi et al., “Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes,” BMC Bioinformatics, 6:126, May 2005. PMID: 15918906 [Online]

V. G. Levitsky et al., “NPRD: Nucleosome Positioning Region Database,” Nucleic Acids Res., vol. 33 (Database issue), pp. D67-70, Jan. 2005. PMID: 15608285 [Online]

Citation. If you use this software in your research, please cite the following paper:

P. Luykx, I. V. Bajić, and S. Khuri, “NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors,” Nucleic Acids Research, vol. 34, Web Server issue, pp. W560-W565, July 2006. PMID: 16845070 [Online]