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Author Topic: Build DNA structures from sequence using command line tools?  (Read 615 times)

Offline vivecalindahl

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Build DNA structures from sequence using command line tools?
« 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

Offline mauricio esguerra

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Re: Build DNA structures from sequence using command line tools?
« Reply #1 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.


Offline vivecalindahl

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Re: Build DNA structures from sequence using command line tools?
« Reply #2 on: January 31, 2018, 05:39:17 am »
Thank you! Seems to be working and just as easy as I'd hoped!

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.