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Author Topic: force DSSR to treat the loop region as base-pairs  (Read 2764 times)

Offline amirtaghavi

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force DSSR to treat the loop region as base-pairs
« 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 
   

Offline xiangjun

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Re: force DSSR to treat the loop region as base-pairs
« Reply #1 on: April 11, 2021, 05:50:17 pm »
Hi,

Yes, DSSR Pro 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
« Last Edit: April 11, 2021, 06:41:35 pm by xiangjun »

 

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.