How can I detect Z-DNA with 3DNA?

[Valentina]

Hi everyone,

I tried to find the answer in the documentation but I'm a bit confused.
How can I detect the occurrence of Z-DNA in my sequences (that vary widely in length)? I'm interest in detecting the base positions of Z-DNA within the sequences.
Which commands should I use? And how should the input file be formatted?

Thank you for your time,
Valentina

[xiangjun]

Hi Valentina,

3DNA is 3D-structure based, i.e., it starts from a tertiary structure in PDB format. So it is not designed to detect Z-DNA from base sequence alone. Other sequence-based tools may better fit your purpose.

Best regards,

Xiang-Jun