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1

General discussions (Q&As) / Re: How to Run Comparisons between Sequences of Similar Length?

« on: December 24, 2019, 02:20:43 pm »

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?     

2

General discussions (Q&As) / How to Run Comparisons between Sequences of Similar Length?

« on: December 23, 2019, 10:04:24 pm »

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.