Hi everyone,
I used RNAfold to predict RNA second structure. I need to calculate the number of foldbacks for each position, which is a critical parameter ot assess RNA second structure. I got a Ct format file like below.
169 ENERGY = -80.3 1
1 G 0 2 0 1
2 G 1 3 0 2
3 A 2 4 167 3
4 A 3 5 166 4
5 A 4 6 165 5
.........
The first column is position. Can someone inform me what the other 4 columns represent? In addition the thermodynamic feature for this RNA is as follows. I need to make statistics of each site's entropy value. Are those values listed at the last column entropy values? I saw a reference uses bits as the unit of entropy. How to calculate entropy?
External loop : -30
Interior loop ( 3,167) AU; ( 4,166) AU: -90
Interior loop ( 4,166) AU; ( 5,165) AU: -90
Interior loop ( 5,165) AU; ( 6,164) GC: -210
Interior loop ( 6,164) GC; ( 9,161) UA: 0
.........................
Hairpin loop ( 81, 87) CG : 430
GGAAAGGCUUUGUAAAACACACUAUUUGACAGUUUGGAAAGCGUGCUCACGGAAAACGAGGGAGCAGCCAAGGCAUUGUUCUUACCGGUUUAUGAAUUGGCUACUUCCUCGUUUUCCGUAAACACGCUUCCCGAGCUUCUAAACGGUGUGUUUCUUGCAAAAACUUUAU
..((((..(((((((((((((((.((((..(((((((.(((((((...((((((((((((((((.((((((..(((...((.....))...)))..)))))).))))))))))))))))...))))))).)))))))..)))).))))))))..)))))))..)))).. (-80.30)
THANK YOU VERY MUCH!
Can you please change question title to something more descriptive?
Thank you very much. Next time i will use more descriptive titles.
"I need to make statistics of each site's entropy value" - This is different question. And what do you mean by "site" and "statistics"?
sorry for my English. actually i mean to get each site's entropy value (this value outputed by RNAfold) for a given miRNA. Next step i need to make statistics of each site's entropy value for many miRNAs. It's much likely the stem and hairpin differs significantly. THANKS!