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Author Topic: automatically count the number of nucleotides involved in RNA helices  (Read 714 times)

Offline elodiem

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Hello,
I have determined reactivities of approximately 2000 nucleotides of several RNA samples using SHAPE and generated dot bracket files. I am able to fold RNAs using these reactivities using RNA structure but I also would like to automatically determine the position and the number of nucleotides involved in helices. Is it possible to do this type of analysis with a software?

thanks for your help

Offline xiangjun

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Hi,

It is not completely clear to me what you want to achieve, based on the information provided. However, DSSR is unlikely to be the tool you are looking for since DSSR takes a 3D structure as its starting point.

If you already have the 2nd structure in dot-bracket notation (DBN), I’d assume the nucleotides in matached () are involved in helices. Right?

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

Offline elodiem

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Hello,
yes it is right. I just want to generate an excel file telling me exactly the number of nucleotides per helices to do some statistic. Do you think it is possible?
thanks

Offline xiangjun

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It should be possible. RNAstructure or ViennaRNA package may already have some utility, or you may need to write some code to parse the DBN to get what you want. As mentioned before, DSSR do not have such functionality.

Best regards,

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

 

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.