3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: elodiem on July 26, 2018, 10:11:31 pm

Title: automatically count the number of nucleotides involved in RNA helices
Post by: elodiem on July 26, 2018, 10:11:31 pm: 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
Title: Re: automatically count the number of nucleotides involved in RNA helices
Post by: xiangjun on July 26, 2018, 11:40:00 pm: 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
Title: Re: automatically count the number of nucleotides involved in RNA helices
Post by: elodiem on July 27, 2018, 06:55:37 am: 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
Title: Re: automatically count the number of nucleotides involved in RNA helices
Post by: xiangjun on July 27, 2018, 09:23:28 am: 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