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Author Topic: Internal loops  (Read 1612 times)

Offline cigdem

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Internal loops
« on: June 29, 2016, 02:52:33 pm »
Hi Xiang-Jun,

I need to gather some information on internal loops and I believe DSSR would be a great tool for this purpose.
What I need is for example for 1E7K:

1) Length of the unpaired regions as you give in internal loops section:

****************************************************************************

List of 2 internal loops

   1 asymmetric internal loop: nts=11; [5,2]; linked by [#1,#2]

     nts=11 CAAUGAGCGAG C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.C42,C.G43,C.A44,C.G45

       nts=5 AAUGA C.A29,C.A30,C.U31,C.G32,C.A33

       nts=2 GA C.G43,C.A44

2) Nucleotide numbers of first and last pairs of the helices as you give in the kink turns section (but I need this info for non kink-turns, too):

****************************************************************************

List of 2 possible kink turns

   1 Normal k-turn with GA on helix#1 (same as C- and NC-helix); iloop#1

      C#1[CG C.C28,C.G45] [GA C.G32,C.A44] NC#2[CG C.C42,C.G34]

      strand1 nts=10; GCCAAUGAGG C.G26,C.C27,C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.G35

      strand2 nts=7; CCGAGGC C.C41,C.C42,C.G43,C.A44,C.G45,C.G46,C.C47


3) Length of the helices as you give in the stems section:


****************************************************************************

List of 4 stems

  Note: a stem is defined as a helix consisting of only canonical WC/wobble

        pairs, with a continuous backbone.

      stem#number[#helix-number containing this stem]

      Other terms are defined as in the above Helix section.

      --------------------------------------------------------------------

  stem#1[#1] bps=3

      strand-1 5'-GCC-3'

       bp-type    |||

      strand-2 3'-CGG-5'

      helix-form  AA

   1 C.G26          C.C47          G-C WC           19-XIX    cWW  cW-W

   2 C.C27          C.G46          C-G WC           19-XIX    cWW  cW-W

   3 C.C28          C.G45          C-G WC           19-XIX    cWW  cW-W

  --------------------------------------------------------------------------

  stem#2[#1] bps=2

      strand-1 5'-GG-3'

       bp-type    ||

      strand-2 3'-CC-5'

      helix-form  .

   1 C.G34          C.C42          G-C WC           19-XIX    cWW  cW-W

   2 C.G35          C.C41          G-C WC           19-XIX    cWW  cW-W

  --------------------------------------------------------------------------

So, for 1E7K the information would be like:

1E7K C 5 2 28 45 42 34 3 2

I need this information also for other internal loops that don't have a kink-turn. Do you think it is applicable?
Thanks a lot.

Cigdem Bayrak

Offline xiangjun

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Re: Internal loops
« Reply #1 on: June 29, 2016, 08:52:18 pm »
Hi Cigdem,

Thanks for your request. It makes sense to add a new field (maybe termed "summary") that collects the info you need for each DSSR-identified loop. I'll look into the issue and report back when the requested feature is implemented (presumably within this week).

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cigdem

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Re: Internal loops
« Reply #2 on: June 30, 2016, 11:33:00 am »
Hi Xiang-Jun,

That is great! Thanks a lot.

Sincerely,
Cigdem Bayrak

Offline xiangjun

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Re: Internal loops
« Reply #3 on: July 07, 2016, 01:29:44 pm »
Hi Cigdem,

I've added a new field, termed "summary", to all DSSR-derived loops. Now the results (using 1e7k as an example) are as below:
# x3dna-dssr -i=1e7k.pdb

   1 asymmetric internal loop: nts=11; [5,2]; linked by [#1,#2]
     summary: [2] 5 2 [C.28 C.45 C.34 C.42] 3 2
     nts=11 CAAUGAGCGAG C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.C42,C.G43,C.A44,C.G45
       nts=5 AAUGA C.A29,C.A30,C.U31,C.G32,C.A33
       nts=2 GA C.G43,C.A44
   2 asymmetric internal loop: nts=11; [5,2]; linked by [#3,#4]
     summary: [2] 5 2 [D.28 D.45 D.34 D.42] 3 2
     nts=11 CAAUGAGCGAG D.C28,D.A29,D.A30,D.U31,D.G32,D.A33,D.G34,D.C42,D.G43,D.A44,D.G45
       nts=5 AAUGA D.A29,D.A30,D.U31,D.G32,D.A33
       nts=2 GA D.G43,D.A44

Note that I've put the number of stems in the first set of [] and closing (canonical) pairs in the second set of [] to make the different sections more distinct. The pairs are designated with chain-id.residue-number to avoid ambiguity (for the most common cases).

While I could introduce an option to output exactly what your described, please consider the above output format for your application. Download DSSR again, and let me know if that fits your bill.

Xiang-Jun



PS:
« Last Edit: July 07, 2016, 04:57:04 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cigdem

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Re: Internal loops
« Reply #4 on: July 08, 2016, 11:30:37 am »
Hi Xiang-Jun,

This is exactly what I needed! Thank you so much for making things so easier.

Just one more thing, if it is applicable could you please also add kink-turn information at the end of the summary line? So that if the corresponding internal loop has a kink-turn, it will say "kt" maybe?

Thank you again.

Best regards,
Cigdem


Offline xiangjun

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Re: Internal loops
« Reply #5 on: July 08, 2016, 04:11:51 pm »
Hi Cigdem,

Quote
This is exactly what I needed! Thank you so much for making things so easier.
Glad that it helps! Note also that questions/requests like yours are one of the driving forces that push 3DNA/DSSR forward. So thank you for using DSSR and posting your questions on the 3DNA Forum.

Quote
Just one more thing, if it is applicable could you please also add kink-turn information at the end of the summary line? So that if the corresponding internal loop has a kink-turn, it will say "kt" maybe?
Yes. If you download the DSSR again, and run it on 1e7k, the corresponding summary lines would now be as below:

List of 2 internal loops
   1 asymmetric internal loop: nts=11; [5,2]; linked by [#1,#2]
     summary: [2] 5 2 [C.28 C.45 C.34 C.42] 3 2 k-turn:normal
     nts=11 CAAUGAGCGAG C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.C42,C.G43,C.A44,C.G45
       nts=5 AAUGA C.A29,C.A30,C.U31,C.G32,C.A33
       nts=2 GA C.G43,C.A44
   2 asymmetric internal loop: nts=11; [5,2]; linked by [#3,#4]
     summary: [2] 5 2 [D.28 D.45 D.34 D.42] 3 2 k-turn:normal
     nts=11 CAAUGAGCGAG D.C28,D.A29,D.A30,D.U31,D.G32,D.A33,D.G34,D.C42,D.G43,D.A44,D.G45
       nts=5 AAUGA D.A29,D.A30,D.U31,D.G32,D.A33
       nts=2 GA D.G43,D.A44

Since the "summary" field is applied to all DSSR-derived loops, in the future it may contain other relevant useful info for non-k-turn loops as well.

Please let me know if you have any idea to fine-tune the formatting etc. I'm planning a new DSSR release (v1.5.8-2016jul09).

Best regards,

Xiang-Jun


PS. Did you know that you can easily parse DSSR output using the --json option? For example,
Code: [Select]
x3dna-dssr -i=1e7k.pdb --json | jq .iloopsThe utility program jq is "a lightweight and flexible command-line JSON processor".
« Last Edit: July 08, 2016, 04:38:52 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cigdem

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Re: Internal loops
« Reply #6 on: July 11, 2016, 02:50:44 pm »
Dear Xiang-Jun,

Thank you for your collaboration. It is perfect!

I agree that in the future you may add information about other motifs as well.

No, I didn't know --json option. It will be so helpful. Thank you for letting me know.

Best regards,

Cigdem

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.