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Author Topic: DSSR - List of bases involved in hairpins?  (Read 4831 times)

Offline jyvdf3asdg2

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DSSR - List of bases involved in hairpins?
« 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]

Offline xiangjun

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Re: DSSR - List of bases involved in hairpins?
« Reply #1 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
« Last Edit: March 13, 2013, 03:33:15 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline xiangjun

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Re: DSSR - List of bases involved in hairpins?
« Reply #2 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, 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 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
« Last Edit: March 14, 2013, 11:24:39 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline jyvdf3asdg2

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Re: DSSR - List of bases involved in hairpins?
« Reply #3 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.

 

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.