3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: jyvdf3asdg2 on March 12, 2013, 06:21:24 pm

Title: DSSR - List of bases involved in hairpins?
Post by: jyvdf3asdg2 on March 12, 2013, 06:21:24 pm: Hi,

Really liking DSSR. I was wondering if there was any way you can have it expressly state the bases involved in the hairpins instead of implied by the closing base pair? The same way you do for 4-way junctions.

Quote
1 4-way junction loop: 16 nts; [2x1x5x0]; linked by [#1, #2, #3, #4]
T.G7+T.U8+T.A9+T.G10+T.C25+T.A26+T.C27+T.G43+T.G44+T.G45+T.G46+T.G47+T.C48+T.G49+T.U65+T.C66 [GUAGCACGGGGGCGUC]
Title: Re: DSSR - List of bases involved in hairpins?
Post by: xiangjun on March 12, 2013, 06:40:11 pm: Thanks for your feedback. I will get DSSR updated in a couple of days, where the requested info will be added to hairpin loops. In the meantime, please test DSSR more thoroughly and report back your thoughts that would make it better tool from a user's perpective.

Best regards,

Xiang-Jun
Title: Re: DSSR - List of bases involved in hairpins?
Post by: xiangjun on March 14, 2013, 03:29:27 pm: I've just updated DSSR to beta-r04-on-20130314. Among other things, now all nucleotides in hairpin loops are explicitly listed in addition to information reported before. So for 1msy (http://www.rcsb.org/pdb/explore/explore.do?structureId=1msy), the new output looks like below:

Code: [Select]
List of 1 hairpin loop(s) 1 nts=4 GUAA closed by pair {A.C2658+A.G2663 [CG], #-1} A.C2658+A.G2659+A.U2660+A.A2661+A.A2662+A.G2663 [CGUAAG]
I have some reasons to report hairpin loops differently from other types of loops (bulges, internal loops, junctions), one being to follow the convention. For example, at first glance, one would immediately see that 1msy (http://www.rcsb.org/pdb/explore/explore.do?structureId=1msy) contains a GUAA tetra-loop (of the most common GNRA type).

I am not aware of a consistent way to name other loops in the literature of RNA structures, so I've come up with my own convention. I'd like to hear what the community has to say when DSSR gains more popularity in the RNA structural world, and make adjustments accordingly.

HTH,

Xiang-Jun
Title: Re: DSSR - List of bases involved in hairpins?
Post by: jyvdf3asdg2 on March 14, 2013, 07:57:31 pm: That is amazing, thanks so much! Works like a charm.

Will let you know if I see anything amiss as I look at more and more secondary structures.