Phase: nucleosome formation site prediction


  1. Objective and History
  2. Theoretical Model
  3. Input Data Description
  4. Output Data Description
  5. Detailed Description of Operations to Run the Program
  6. Example
  7. Reference
  8. Concluding Notes and Communications

1. Objective and History

The program Phase designed for prediction of nucleosome formation sites.

2. Theoretical Model

The Phase method measured the abundance of phased (periodic) dinucleotides in a nucleotide sequence implying the DNA double helix periodicities (~10.5 bp per turn). The method was based on the comparison of probabilities of phased dinucleotides occurrences with those expected by chance. PWM-based score [1] calculated by the observed occurence of periodic/aperiodic dinucleotides. At the next step the contionous wavelet transformation [2] finds the peaks of the PWM-score profile. The detailed description of algorithm can found in [3] (see Supplementary Data for this paper).

3. Input Data Description

The input data for this program are the following: one or multiple sequence(s) in fasta format, designation of the training set in the drop-down menu: "All" denotes of nucleosomal DNA of all species only, "Mam" and "Ysc" refers to mammal and yeast nucleosomal DNA, respectively. The minimal sequence length is equal to 530 bp.

4. Output Data Description

Output data presented in text mode only. The individual profile(s) for each sequence(s) of input data presented as a the list of dyad position and respective scores. The specification of output scores:
1) positive/negative score denotes nucleosome/linker region;
2) score above Thr=0.013 marks stable nucleosomes;
3) positive score below Thr=0.013 means fuzzy (unstable) nucleosome.
Value Thr=0.013 computed as the 50% percentile (median) for whole-genome profile (Human, Rice), i.e. approximately 50% of genome nucleosomal DNA have score above Thr=0.013, in this case the context specificity is supposed.
Dyad means the center of nucleosome formation site.

5. Detailed Description of Operations to Run the Program

1) Enter your nucleotide sequence the inputting sequence box.
2) Designate the model ("All" or "Mam" or "Ysc").
3) Click over [SCAN] and wait for the end of the calculations.

6. Examples

Example gives program application for one sequence.

7. References

[1] Levitsky VG et al. Nucleosome formation potential estimation via dinucleotides periodicity preferences. Proceedings of the sixth international conference on bioinformatics of genome regulation and structure (BGRS'2008), 2008, p. 140.
[2] Lu XQ et al. Maximum Spectrum of Continuous Wavelet Transform and Its Application in Resolving an Overlapped Signal. J Chem Inf Comput Sci 2004,44:1228-1237
[3] Levitsky VG, Babenko VN, Vershinin AV. The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning. J Biomol Struct Dyn. 2014;32(1):115-26.

8. Concluding Notes and Communications

Any comments and questions may be mailed to author - Levitsky

last modified 15.05.2012.

Institute of Cytology and GeneticsLogo

Author: Victor Levitsky
Contributors: Dmitry Rasskazov
Leader: Prof. N.A. Kolchanov

This work is supported by the Ministry of Education and Science of the Russian Federation.

© 2012, IC&G   SB RAS, Laboratory of Theoretical Genetics