Question: Interpreting Structure Conservation Analysis
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gravatar for pld
6.5 years ago by
pld4.8k
United States
pld4.8k wrote:

I am interested in determining if the secondary structure of several large (500bp+) sequences is conserved, with an ultimate goal of demonstrating greater divergence between the NTRs (the sequences here) versus ORFs between species. That is the coding regions have greater conservation than the non-coding. To do this I have been considering using the ViennaRNA services structure conservation analysis (SCA). However, after running the program I am finding the interpretation of the results not obvious to me.

The results can be found here: http://rna.tbi.univie.ac.at/cgi-bin/SCA.cgi?PAGE=3&ID=zwPrc7kAK8&r=36

For example the measure Basepair distance, pairwise provides a z-score of -7.045 with a p-value of zero. Obviously I can reject the null that my sequences are not different than the random sampling performed, but the sign of the value and how it related to conservation is where I am unsure. I pulled some of the papers they cite for the man pages of these programs and my thoughts are coming from those. My thought is that a negative sign would imply that the secondary structure of my sequences is less different than the random samplings. In short, I should interpret a z-score of -7.045 as the secondary structure of the sequences is significantly more conserved than one would expect by chance. Is this the correct interpretation?

conservation rna • 1.5k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 6.5 years ago by pld4.8k
0
gravatar for Leo
6.5 years ago by
Leo120
Hong Kong
Leo120 wrote:

Z-score is described as the extent of standard deviation that the sequence deviates from the mean MFE of the shuffled sequences, I don't think it can be interpret as conservation.

ADD COMMENTlink written 6.5 years ago by Leo120
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