3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Valentina on September 07, 2016, 08:12:03 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage

Title: How can I detect Z-DNA with 3DNA?
Post by: Valentina on September 07, 2016, 08:12:03 am

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

Title: Re: How can I detect Z-DNA with 3DNA?
Post by: xiangjun on September 07, 2016, 08:51:27 am

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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University