Mea - Prediction of maximum expected accuracy RNA secondary structures

Supplemental material of manuscript "The Trouble with Long Range Base Pairs in RNA Folding" by
The Students of the Bioinformatics Computer Lab 2013, Fabian Amman, Stephan H. Bernhart, Gero Dose, Jing Qin, Peter F. Stadler, and Sebastian Will

Software written by Sarah Berkemer and Sebastian Will

Mea was developed as part of the lab class "Bioinformatik von RNA- und Proteinstrukturen (Praktikum, Modul 10-202-2208)". The package predicts maximum expected accuracy (MEA) RNA secondary structures from dot plots of RNAs while correcting the score in dependence of base pair span. Furthermore, it provides tools to evaluate predictions and optimize parameters.


Mea is free software (GNU GPL 3). Please use the newest release unless you know what you are doing. Older releases are available below for reference.

mea-0.6.4 source [tar.gz]
Version 0.6.x adds slide rule and conflicts rule for comparisons to the reference structure; these are turned on by default. 0.6.4 corrects major bugs in the structure comparison of 0.6; the prediction itself is unchanged.

The package can be compiled and installed in the common autotool's way by
   ./configure; make; make install.

Old releases

mea-0.5 source [tar.gz]
Version 0.5 enables comparing two structures w/o folding
(option --structure). Structure comparison is buggy:(

mea-0.4 source [tar.gz]
Version 0.4 has been used to produce the published results.

Mea package tools

Since release 0.5 the tool supports the general comparison of a given "predicted" structure to a "reference" structure by confusion matrix, F1-score, and MCC (Mathew's correlation coefficient.)

Furthermore, the package allows to compile a library; this lib can be imported into R, where it enables optimizing parameters using R functionality.

Please call tools with help option to learn more about their parameters. Dot plots are generally read from files in ViennaRNA's "" format.