The motif library used with --contacts is particular. It was provided by Isaure Chauvot de Beauchêne from the LORIA

laboratory. These motifs are made up of RNA fragments linked to proteins.

Several versions of these designs have been provided, but the most complete is the latest:'motifs_06-06-2021.json' The current scripts were created based on this file, and doesn't work with the other older libraries.

There is also 2 benchmarks files also in json format : 'benchmark_16-06-2021.json' and 'benchmark_16-07-2021.json'. It contains complete RNA sequences that bind to a protein, the first one contains only 33 RNA, and the second one contains 130 RNA.

The benchmark.dbn and benchmark.txt were created based on the 'benchmark_16-07-2021.json'. They are mostly used for the Isaure_benchmark.py script and scripts from the 'scripts' directory.

The motifs_final.json it obtains after executing the count_pattern.cpp script in 'script' directory on the 'motifs_06-06-2021.json' motifs file. This script count the number of "occurrences" of the motif. So we consider that if the sequence of motif A is included in motif B, then for each inclusion of B we also have an inclusion of A. And vice versa.

The motif library used by BiORSEO is the one in the 'bibliotheque_a_lire' directory. There should only be the json file we wish to be used by BiORSEO for it's prediction. That's why you shouldn't put other type of file!