Commit b165d07e authored by Roman Sarrazin-Gendron's avatar Roman Sarrazin-Gendron
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Update README.md

parent 721587b8
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BayesPairing2 comes with three pre-assembled datasets you can immediately start searching sequences with. To search with a specific dataset, use the ``-d`` option with the name of the dataset.
* ``RELIABLE``: A subset of 60 modules from the RNA 3D Motif Atlas with the highest number of occurrences and highest sequence variation. We are confident in the prediction of those modules given the high quality data we have to train them. This is the default dataset we use.
* ``RELIABLE``: A subset of around 60 modules from the RNA 3D Motif Atlas with the highest number of occurrences and highest sequence variation. We are confident in the prediction of those modules given the high quality data we have to train them. This is the default dataset we use.
* ``ALL``: A dataset containing all the modules we were able to convert from the 3D Motif Atlas to BayesPairing2 models (426). Some of those only had one occurrence and/or may have been trained on limited/incomplete data.
* (DEPRECATED) ``rna3dmotif`` : A dataset containing the 75 most recurrent modules as identified via an exhaustive search of loops in the full PDB database with rna3dmotif.
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BayesPairing2 returns results by index, where the indexes correspond to modules in the relevant database.
The 3D Motif Atlas modules match to entries in that database. The details of the database can be found in ``bayespairing/models/``.
The 3D Motif Atlas modules match to entries in that database. The details of the database can be found in ``bayespairing/DBData/``.
In this csv file, you can observe that sometimes, more than one module maps to the same entry of the Atlas; this is because the 3D Motif Atlas modules are clustered in 3D, and sometimes it is not possible to represent all occurrences accurately with the same graph, so they must be searched separately.
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