Feature calculation: MFEI3 - Githubissues

OstfriesenBI / PredmiRNA

A set of scripts and tools to train a classifier for pre-miRNA Recognition

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Feature calculation: MFEI3 #23

Closed mariusrueve closed 5 years ago

mariusrueve commented 5 years ago

MFE Index 3 (MFEI3)

MFEI3 = dG/n _loops

dG/L: Gibbs free energy divided by the length of the sequence
n_loops: the number of loops in the secondary structure

Input: csv file with MFE/L and n_loops

"comment","dG/sequencelength","n_loops"
"test","-29.90/24","1"

Output: csv file with comment & mfei3

"comment","mfei3"
"test","xxx"

Finesim97 commented 5 years ago

The number of loops should be derived from the secondary structure. I am not sure, how you get the number of loops from it: ....((((((..(((((..((((((..(((.((.....)).))))))))))))))....))))))............((((((......)))))).

mariusrueve commented 5 years ago

If [amount of (] == [amount of )] the loop is closed and loops+1. Therefore we maybe need an extra script to count the loops, if we don't find another solution.