# NEsted MOnte Carlo RNA puzzle solver (NEMO)

Create a 'nemo' folder inside a ViennaRNA 2.1.x source code tree

~/ViennaRNA-2.1.9$ mkdir nemo

copy the 3 files into that folder, then compile with

$ gcc -g -O2 -fopenmp -I../H -MD -MP -c -o nemo.o nemo.cpp
$ gcc -g -O2 -fopenmp -L../lib -o nemo nemo.o -lstdc++ -lRNA -lm -ldl

Run with

$ ./nemo [-E] [-v] [-i <num_iter>] "<target_structure>" [<start_sequence>]

Sequentially run full test on Eterna100:

$ cat list.e100 | xargs -L 1 ./nemo -E -v

Heuristics and strategies used in the application are described at
https://docs.google.com/document/d/13_rwbrBc9H5ldeLISTPw9jPJ1anvTAnkR5DhAyBOdN4/edit

A manuscript describing the NEMO algorithm is available at
https://www.biorxiv.org/content/10.1101/345587v1