Forum: Designing DNA with certain properties, needs access to resource for evaluation and itteration of designs
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gravatar for stian.a.weiseth
5.8 years ago by
stian.a.weiseth0 wrote:

Hello Biostars.

I am looking for a resource to Test and compare DNA sequences based upon certain criteria, I need to know MT and secondary structure and MFE.

My platform is Windows and my programming skill is limited to python only, my efforts to make the wrappers for Vienna RNA work on this platform has been futile.

Is there an existing websource that you can call with an URL containing your DNA and receive these parameters? If not, how would you set this up locally.

Best regards.

Stian A. Weiseth

ADD COMMENTlink written 5.8 years ago by stian.a.weiseth0

RESTful service to provide sequence stats. Hmmm. Why pass the sequence through the URL? That will make processing long sequences a bit difficult.

ADD REPLYlink written 5.8 years ago by _r_am32k

As What I am looking for would be a free service, long sequences and the power they would consume would be decided against in the first place.

A way to call Nupack or a similar resource and just read out the three parameters would be great.

ADD REPLYlink written 5.8 years ago by stian.a.weiseth0

You could always download Nupack and set up a web service where you serve up the results, no?

ADD REPLYlink written 5.8 years ago by _r_am32k

This is intended for commercial use later, but as of right now it is just an experiment, so there is a bit of a grey zone going on. 

ADD REPLYlink written 5.8 years ago by stian.a.weiseth0
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