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Questions and answers > General discussions (Q&As)

Build DNA structures from sequence using command line tools?

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vivecalindahl:
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

mauricio esguerra:
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.

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

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.