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Author Topic: include non-cannonical base-pairing in DBN output?  (Read 251 times)

Offline jms89

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include non-cannonical base-pairing in DBN output?
« on: June 07, 2018, 07:15:28 pm »
Hello, is there a simple way to include include non-canonical base-pairs in the DBN output of DSSR?

Currently, it seems that non-canonical base-pairs are ignored, and those nucleotides are treated as unpaired in the DBN output. I didn't see any simple way of changing this behaviour in the manual, but was wondering if i'm missing something.

Thanks.

Offline xiangjun

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Re: include non-cannonical base-pairing in DBN output?
« Reply #1 on: June 08, 2018, 12:10:55 am »
DBN is a simple, compact way to represent RNA secondary structure, as matched (),[], {} etc of canonical pairs (Watson-Crick and G--U wobble). The DSSR implementation of DBN follows the convention. DBN extensions that account for non-canonical pairs have been reported in the literature. No standard representation of such extensions exists, as far as I know.

In addition to non-canonical pairs, triplets and quadruplets (or higher, generally termed multiplets in DSSR) also exist in RNA, but they cannot be properly represented by DBN either. I'm generally in favor of keeping DBN simple in DSSR, at least by default. However, I'd consider expanding DBN by additional options, if necessary. I can be easily convinced by seeing concrete/worked examples.

Xiang-Jun
« Last Edit: June 08, 2018, 12:16:13 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline jms89

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Re: include non-cannonical base-pairing in DBN output?
« Reply #2 on: June 08, 2018, 02:04:30 pm »
Thanks, I was just wondering if there was a quick solution - my use case is quite specific, but it relates to visualization. I believe I can just parse the .ct output and generate my own DBN fairly easily.

Offline xiangjun

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Re: include non-cannonical base-pairing in DBN output?
« Reply #3 on: June 09, 2018, 07:43:19 pm »
You're welcome to post your code, with worked examples, to the section "Users' contributions". Your use case may be quite specific right now, from your perspective. Others in the community, however, could also benefit from your effort (probably in the long run). The 3DNA Forum could help build "an online community for DNA/RNA structural bioinformatics".

Best regards,

Xiang-Jun
« Last Edit: June 09, 2018, 07:45:33 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.