How to Run Comparisons between Sequences of Similar Length?

[HenryB]

I have an interest in comparing all the many parameters calculated by 3dna for the following dinucleotides: CG, CA, CT, and CC. Is there someplace in this software package where I might enter these base pair steps and end up with comparisons between the variables? As for example, a rank ordering of these base pairs on the parameters of propeller twist or shift or slide or torsion angles? I'm looking for data like: Propeller Twist: CC > CT, CT = CA, CA > CG. 

[xiangjun]

Sorry, the simple answer is no.

The various parameters associated with each step are context dependent. If you are interested in the trend of certain parameters, you could run 3DNA on your specific dataset, and then extract those parameters for comparison.

Best regards,

Xiang-Jun

[HenryB]

Professor Xiangjun,
Respectfully, the tetranucleotide sequence ACGG is much more likely to undergo a double strand break under the influence of an ultrasound energy field than the tetranucleotide sequence CAGG. I know I can calculate a large number of parameter values for each of these tetranucleotides using 3DNA. I need to know which one of the parameters plays the most important role in the process of double strand breaking. Is it Propeller Twist? Roll? Alpha or Beta torsion bond angles?     

[xiangjun]

Is it Propeller Twist? Roll? Alpha or Beta torsion bond angles?

Interesting questions. Unfortunately, I do not have an answer as to how these parameters (if any) may be related to your research question. You'd need to explore the issue and see what comes out.

Best regards,

Xiang-Jun