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Author Topic: How 3DNA-DSSR define RNA junctions?  (Read 6330 times)

Offline hume

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How 3DNA-DSSR define RNA junctions?
« on: January 07, 2015, 12:08:21 am »
Dear developer,

Hello! I am using 3DNA-DSSR to find junctions in RNA structures, but I am just curious about the criteria for the RNA structure elements to be a junction so that appears in the PDB file:

1) The length of each stem
2) Do other structure elements that do not belong to the junction on the secondary structure level but is close to the junction on the tertiary structure level count?

I do appreciate your help!

Thank you so much,
Chen

Offline xiangjun

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Re: How 3DNA-DSSR define RNA junctions?
« Reply #1 on: January 07, 2015, 09:55:36 am »
Hi Chen,

DSSR identifies junctions (and other types of loops, such as hairpin loop, internal loop or bulge) as one would expect when looking at the secondary structure representation. For example, the cover image of the DSSR User Manual for the yeast phenylalanine tRNA (1ehz) shows the 4-way junction in the middle and three hairpin loops at the peripheral. The length of stems do not matter, and a (junction) loop forms a 'topological' circle -- see the DSSR output of the 4-way junction for 1ehz:

Code: [Select]
List of 1 junction
   1 4-way junction: nts=16; [2,1,5,0]; linked by [#1,#2,#3,#4]
     nts=16 UUAgCgCGAGgUCcGA A.U7,A.U8,A.A9,A.2MG10,A.C25,A.M2G26,A.C27,A.G43,A.A44,A.G45,A.7MG46,A.U47,A.C48,A.5MC49,A.G65,A.A66
       nts=2 UA A.U8,A.A9
       nts=1 g A.M2G26
       nts=5 AGgUC A.A44,A.G45,A.7MG46,A.U47,A.C48
       nts=0

More details about the underlying algorithms will be described in the DSSR manuscript I have been focusing on. Stay tuned.

HTH,

Xiang-Jun
« Last Edit: January 07, 2015, 11:33:39 am by xiangjun »

Offline hume

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Re: How 3DNA-DSSR define RNA junctions?
« Reply #2 on: January 07, 2015, 11:54:33 am »
Dear Xiangjun,

Thank you for your reply and your information!  Then in my case I can only test several models and analyze the output. I am looking forward to seeing the details in the coming paper.

Thank you so much,
Chen

 

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.