3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: vivecalindahl on January 31, 2018, 04:16:53 am

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

Title: Build DNA structures from sequence using command line tools?
Post by: vivecalindahl on January 31, 2018, 04:16:53 am

Hi!

I would like to "emulate" the behaviour of the 3DNA webserver, but using command line tools. I.e., I want to input a DNA sequence and output the corresponding pdb using a shell script. Any help of which tools to link together or an example would be much appreciated.

Best,
Viveca

Title: Re: Build DNA structures from sequence using command line tools?
Post by: mauricio esguerra on January 31, 2018, 04:26:20 am

You can download x3dna from:

http://forum.x3dna.org/site-announcements/download-instructions/

And then use fiber to generate any of the available models:

http://x3dna.org/articles/3dna-fiber-models

Then a command like:

    fiber -seq=AAAGGGTTTCCC BDNA.pdb

Will generate a BDNA with that sequence.

Cheers,

M.

Title: Re: Build DNA structures from sequence using command line tools?
Post by: vivecalindahl on January 31, 2018, 05:39:17 am

Thank you! Seems to be working and just as easy as I'd hoped!

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