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RNA-Psyclic

RNA-Psyclic

RNA-Psyclic is a cyclic motifs detection pipeline, making use of MC-Search and MC-Annotate, and producing a nice HTML visualization interface. It's basically your psychic to spot RNA cyclic motifs in multiple PDBs.

It takes two things in input:

  • A set of PDB files: Holds molecules structural information. Motifs will be searched on these.
  • A set of descriptor files: Describes the motif that we're looking for in the molecules.

Usage

Detecting motifs

  • Place your motif descriptor files in the motif directory
  • Place your PDB files in the pdb directory
  • From the project root directory, launch the pipeline with the following command:
python ./rna-psyclic.py

What will happen goes as follow:

  • RNA-Psyclic runs MC-Search on all PDB files, using all descriptors. It produces PDB files containing the list of motifs detected for a descriptor.
  • Motifs PDBs are fed to MC-Annotate, that will infer residue interactions composing the cycles.
  • The output of MC-Annotate is then converted to JSON documents, one per PDB-descriptor combination.
  • All JSON are collated into one big JSON database.
  • A string describing the cyclic motif type is computed, when possible.
  • The final JSON database is moved to the webapp directory.

It is then possible to visualize the results in the web application.

Using the web application

  • Go to the webapp folder, and start Python's SimpleHTTPServer:
cd webapp
python -m SimpleHTTPServer

  • Open your web browser to the provided URL, such as: http://127.0.0.1:8000/. From there, you can then explore the JSON database.

  • It's possible to re-execute the pipeline by adding more motifs and PDB files in their respective folders. Re-launching the pipeline will only compute what's missing, instead of redoing everything.

Scripts

The following scripts have been developed for RNA-Psyclic:

rna-psyclic.py

The main pipeline execution script, builds a JSON database of motifs defined in motif folder, for PDB files provided in pdb folder.

mc-annotate_to_json.py

Converts the output of MC-Annotate to a JSON document.

merge_json.py

Merges all motif descriptor/PDB JSONs in the folder structure produced by rna-psyclic.py.

set_motif_type.py

Attempts to compute a cycle type string, as suggested in Lemieux-Major 2006. (L=Link, P=Pair, S=Stack)

Future plans

  • Running multiple instances of MC-Search by providing a number of threads with the parameter --threads
  • Detecting errors in provided descriptor files, by flagging if there is found motifs that could be broken into smaller pieces.