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Questions and answers => RNA structures (DSSR) => Topic started by: lijun on March 06, 2019, 04:25:43 pm

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Title: Junction definition
Post by: lijun 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

Title: Re: Junction definition
Post by: xiangjun on March 06, 2019, 04:53:52 pm

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

Title: Re: Junction definition
Post by: lijun 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

Quote from: xiangjun on March 06, 2019, 04:53:52 pm

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

Title: Re: Junction definition
Post by: xiangjun on March 07, 2019, 11:20:56 am

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

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

Quote

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

Title: Re: Junction definition
Post by: lijun on March 07, 2019, 02:23:01 pm

--nested option works!
Thanks,
Jun Li

Quote from: xiangjun on March 07, 2019, 11:20:56 am

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

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

Quote

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

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