by Victor G. Levitsky

 Contents:

1. Objective and History

2. Theoretical Model and Data Presentation

3. Input Data Description

4. Detailed Description of Operations to Run the Program

5. Profile Examples

6. References

7. Concluding Notes and Communications

1. Objective and History

Main aim of the program is visualizing DNA sequence bending stiffness properties. The current program is a modified version of the original program by Levitsky developed in 1997 and used for description of nucleosomal DNA sequences.

2. Theoretical Model and Data Presentation

Program generates a profile of DNA bending stiffness energy from the base step parameters for DNA persistence length [1]. These parameters were taken from an empirical correlation between melting temperature data and persistent length values for synthetic DNA polymers [1]. The profile demonstrates that the energy E of DNA bending stiffness within a certain DNA region depends on the position X of the region center along the sequence. Values E for every such region (scanning window W) are calculated as the sum of base step parameters. The output data E(X) are presented in the simple chart form.

3. Input Data Description

The input data for this program are the following: sequence Length L, Window size W, Start position SP and End positions EP. To run the program correctly, these values should be defined within certain limits:

• sequence Length L should not be less than 2 base pairs (bp);
• Window W ranges from 2 bp to L (more precisely up to EP-SP);
• Start position SP may vary from 0 to L-W;
• End position EP may be from SP+W to L.

The program provides the following list of default input parameters:

• Sequence Length L equal to the length of all inputtted sequences;
• Window size W=2 bp;
• Start position SP=0;
• End position EP=L.

All default parameters used for calculation are placed below the inputting sequence box. Any of these values can be modified within certain limits. The exceeding of the limits results in a warning and restoring the default values. The extreme values elicit error messages and requests to enter more reasonable values. The calculation can be performed only after the input of reasonable values. Note that the clicking of the button [RESET] will restore all default values.

4. Detailed Description of Operations to Run the Program

Profile presentation for any nucleotide sequence can be obtained as follows:

1) Enter your nucleotide sequence using lowercase letters (for example, atgc) in the inputting sequence box. Alternatively two data sources are available: ID or AC from database otherwise http or ftp address of file with formats.

2) Click over [EXECUTE] and wait for the end of the calculations.

3) The derived chart can be saved as a GIF image by clicking it context menu.

5. Profile Examples

shown Below as examples are three profiles calculated by the program for DNA sequence of nucleosomal site from nucleosomal DNA database [2]. Window sizes are 10, 30, and 50 bp. It is evident that, using these program, the particularities of DNA bending stiffness landscape can be seen as the local profile's maximum or minimum.

6. References

[1] Sivolob A.V., Khrapunov S.N. // J. Mol. Biol. 1995. V. 247. P. 918-931.

[2] Ioshikhes I., Trifonov E.N. // Nucl. Acids Res. 1993. V. 21. P. 4857-4859.

6. Concluding Notes and Communications

Over past few years, a lot of utility programs and display tools has appeared in response to special needs of numerous users. So users are encouraged to communicate any suggestions or particular desires by electronic mail to:

Levitsky

last modified 28.11.97.