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Questions and answers => RNA structures (DSSR) => Topic started by: kailsen on March 10, 2013, 01:07:27 am

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Title: What are the definitions of helix, stem, step etc in DSSR?
Post by: kailsen on March 10, 2013, 01:07:27 am
Hi Lu,
 I have downloaded the DSSR program and above to use it. I will be using to find. pseudo helices. I want to know. what is consideres as an helice? a stem? a step? step has two basepairs. at what level it will be pushed to be called as stem. i see that in ur sample output, the acceptor arm fully will be called helices. am i correct?.
Title: Re: What are the definitions of helix, stem, step etc in DSSR?
Post by: xiangjun on March 10, 2013, 10:44:05 am
Thanks for downloading the beta testing version of DSSR. I am working on a manuscript, and more details will be made available in due course. In the meantime, here is a short answer to your questions:


The default settings currently adopted in DSSR are based on my understanding of the conventions in the RNA structural world. I'd like to hear what users have to say and will make refinements accordingly. More functionality will be added the DSSR; with the current beta release, I've just kicked the ball rolling. Based on experience of supporting 3DNA and using other bioinformatics tools, I've created DSSR from the ground up to be trivial to set up and easy to use. Just play with it, and report back any issues you have.

HTH,

Xiang-Jun

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.