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Questions and answers => RNA structures (DSSR) => Topic started by: jms89 on June 07, 2018, 07:15:28 pm

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Title: include non-cannonical base-pairing in DBN output?
Post by: jms89 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.

Title: Re: include non-cannonical base-pairing in DBN output?
Post by: xiangjun 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

Title: Re: include non-cannonical base-pairing in DBN output?
Post by: jms89 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.

Title: Re: include non-cannonical base-pairing in DBN output?
Post by: xiangjun on June 09, 2018, 07:43:19 pm

You're welcome to post your code, with worked examples, to the section "Users' contributions (http://forum.x3dna.org/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

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