Topics

1

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
     

     

2

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

3

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

4

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