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Questions and answers => RNA structures (DSSR) => Topic started by: amirtaghavi on April 11, 2021, 05:13:23 pm

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Title: force DSSR to treat the loop region as base-pairs
Post by: amirtaghavi on April 11, 2021, 05:13:23 pm

Hello Dr. Xiang-Jun,

I am using the DSSR to analyze a RNA structure (54 bps) with multiple repeats of (AUUCU) seq incorporating multiple 3x3 internal loops. As the structure is highly dynamic, many of the loops do not satisfy the conditions needed to be treated as a base-pair and naturally are skipped by the DSSR.
is there any way, other than manipulating the parameters which are used in DSSR to account for a base-pair, to force the DSSR to analyze all the 54 base-pairs irrespective of the defined criteria for base-pairs.

Thanks for your help.

Best,
Amir 
   

Title: Re: force DSSR to treat the loop region as base-pairs
Post by: xiangjun on April 11, 2021, 05:50:17 pm

Hi,

Yes, DSSR Pro (http://innovation.columbia.edu/technologies/CU20391) can do it. DSSR Pro also includes many advanced features, enhanced usability, and support that are not available in the basic version.

Best regards,

Xiang-Jun

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