Messages

1

RNA structures (DSSR) / Re: Wrong junctions

« on: September 17, 2019, 04:05:43 pm »

Hi Xiang-jun,
      Even with --nested option, some RNAs still share the same helix. They are 3j7r, 5mrc, 5mre, 5mrf, 6ost.
      Best,
Jun

2

RNA structures (DSSR) / Wrong junctions

« on: September 17, 2019, 11:48:56 am »

Hi Xiang-jun,
     When I used  dssr to extract junctions, I found the junctions for some RNAs share the same stem.
     For example, for RNA 4wsm, the output is:
          1* 3-way junction: nts=10; [0,4,0]; linked by [#100,#101,#101]
          60* 4-way junction: nts=17; [3,1,1,4]; linked by [#211,#212,#282,#212]
          76* 5-way junction: nts=14; [0,0,1,3,0]; linked by [#332,#333,#335,#333,#334]
      I used the latest version (1.9.6) of dssr, and the command as follows:
          x3dna-dssr -i=4wsm.cif -auxfile=no --isolated-pair=not-in-loop -idstr=long -o=4wsm.out
 
        Thanks and best wishes,
Jun
     

     

3

RNA structures (DSSR) / Re: DSSR of 32 bit version

« on: August 28, 2019, 12:23:46 pm »

Hi Xiang-Jun,
     Thank you very much and it is working now.
     We are implementing a web server to predict SHAPE reactivity from RNA 3D structure. Since the 2D structure is necessary to predict the SHAPE profile from a structure, we are using the DSSR module to extract the 2D structure from a 3D structure file. We hope that our server will help users integrate experimental SHAPE data to guide their RNA structure prediction. The 3D Structure-SHAPE Relationship (3DSSR; named similarly to your program) model was previously reported in "Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis".
      Thanks again for your kind help.
Jun

4

RNA structures (DSSR) / Re: DSSR of 32 bit version

« on: August 28, 2019, 10:52:34 am »

Hi Xiang-Jun,
     Thanks for your reply.
      Previously I used DSSR on my own computer, but now we need to install it on an old server which uses a 32 bit OS.
      If it is too much time and effort for you, we can pull jobs from the server to run locally, posting the results to the server after the jobs finish. However, this will cause slowdowns for users of our server since the jobs can be run very fast on the external server.
     If you can compile a 32 bit version for us, we would appreciate the help, but if it takes you a lot of time, we can find a sub-optimal workaround.
     Thanks again and best regards,
Jun

5

RNA structures (DSSR) / Re: DSSR of 32 bit version

« on: August 27, 2019, 05:46:04 pm »

Hi Xiang-Jun,
     I am using linux OS (centos 6.9).
     Thanks for your prompt reply.
Jun

6

RNA structures (DSSR) / DSSR of 32 bit version

« on: August 27, 2019, 05:01:12 pm »

Hi Xiang-Jun,
     The DSSR of the latest version cannot be used on 32 bit OS. I am wondering if you can provide the executable of 32 bit version or the source code.
     Thanks for your help and best,
Jun

7

RNA structures (DSSR) / Re: Junction definition

« on: March 07, 2019, 02:23:01 pm »

--nested option works!
Thanks,
Jun Li

OK. I got it. I'll look into the issue.

Regarding the definition of (junction) loops, the DSSR paper says:

In DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C).

The situation becomes less intuitive/obvious when pseudoknots are included. You could try the --nested option to removed pseudoknots to see if the results make more sense.

Best regards,

Xiang-Jun

8

RNA structures (DSSR) / Re: Junction definition

« on: March 07, 2019, 11:07:43 am »

Hi Xiang-Jun,

I used the option -loop-exclude-icpair.  In my previous post “Stems of junction structure have only one base pair”, You told me to use this option to exclude icPairs from loops.

Thanks,

Jun Li

Hi,

I cannot reproduce your reported result based on information provided (i.e., PDB id: 4gma). Could you please be more specific by attached the PDB file, DSSR version, and options you used?

Thanks,

Xiang-Jun

9

RNA structures (DSSR) / Junction definition

« on: March 06, 2019, 04:25:43 pm »

Hi,

I find that dssr treats some pseudoknots as junctions. For example in rna 4gma:
   List of 3 junctions
   1 3-way junction: nts=8; [2,0,0]; linked by [#6,#13,#7]
     summary: [3] 2 0 0 [Z.74 Z.81 Z.201 Z.193 Z.194 Z.80] 2 4 5
     nts=8 GCGAUCGC 1..Z.G.74.,1..Z.C.75.,1..Z.G.200.,1..Z.A.201.,1..Z.U.193.,1..Z.C.194.,1..Z.G.80.,1..Z.C.81.
     nts=2 CG 1..Z.C.75.,1..Z.G.200.
     nts=0
     nts=0
The stem number [#6,#13,#7] is not in the ascending order. Can I filter out these false junctions by checking the order of the stems?

Thanks,
Jun Li

10

RNA structures (DSSR) / Re: Stems of junction structure have only one base pair

« on: January 16, 2019, 11:43:47 am »

Hi Xiang-Jun,

Thanks for your prompt reply and help.

Jun Li

Hi Jun Li,

Thanks for using DSSR and for posting your questions on the 3DNA Forum.

I understand that the inclusion of isolated canonical pairs (icPairs, those with negative index numbers) in delineating loops may lead to 'spurious' (junction) loops. I am so glad that this issue has been finally brought up on the Forum.

As far as I know, no consensus exists as to whether icPairs should be (always) included in the delineation of loops. Without taking them into consideration, however, the widely documented GUAA tetraloop in PDB entry 1msy (see figure below) cannot be logically identified. That's why DSSR counts icPairs in loops, by default.

While undocumented, DSSR has an option to exclude icPairs from loops, i.e. (--loop-exclude-icpair). Run DSSR with this option on your example PDB entry 5vyc, you'd find that the 3-way junction you reported is gone.

In a similar way, it is also debatable if a non-canonical base pair in an otherwise 'regular' double helix should be taken as part of a stem or as an internal loop. As noted in the 2015 DSSR paper in NAR:

Following standard conventions (13,35–36), DSSR by default uses only canonical pairs to identify stems and to characterize pseudoknots. Nevertheless, the program contains provisions for including noncanonical pairs in an extended definition of stems

It is my hope that DSSR would help 'standardize' the field, probably in the long run.

Best regards,

Xiang-Jun

11

RNA structures (DSSR) / Stems of junction structure have only one base pair

« on: January 15, 2019, 08:27:34 pm »

Hi all,

I am using the newest DSSR to extract the junction structure, but the stems of some junctions have only one base pair. Take 5vyc.cif for an example and one of its 3-way junctions is as follows:

   1 3-way junction: nts=11; [2,1,2]; linked by [#63,#64,#-49]
     summary: [3] 2 1 2 [i2.1225 i2.1641 i2.1228 i2.1530 i2.1532 i2.1638] 5 3 1
     nts=11 UGGAUACGGAA 1..i2.U.1225.,1..i2.G.1226.,1..i2.G.1227.,1..i2.A.1228.,1..i2.U.1530.,1..i2.A.1531.,1..i2.C.1532.,1..i2.G.1638.,1..i2.G.1639.,1..i2.A.1640.,1..i2.A.1641.
       nts=2 GG 1..i2.G.1226.,1..i2.G.1227.
       nts=1 A 1..i2.A.1531.
       nts=2 GA 1..i2.G.1639.,1..i2.A.1640.

The last stem #-49 has only one base pair. There are many cases like this in the output. Is it reasonable to take structure like this as a junction?

Thanks,

Jun Li