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RNAQUA

RNAQUA (RNA QUality Assessment) is a web service based wrapper of basic RNA comparison metrics. It is a RESTful web service client developed in Java. The tool provides a set of web services initially designed for RNAssess (Lukasiak et al., Nucleic Acids Research, 2015;43(W1):W502-W506. doi:10.1093/nar/gkv557) to support the quality assessment of RNA 3D structures. RNAQUA requires a stable release of JRE 7 (or later) installed on a user workstation with an internet access. Full implementation of the tool is stored on github and maintained by Antczak. The binaries and use cases can be downloaded from here. Most important features of RNAQUA:

  • At the input, a user provides RNA 3D structure(s) in PDB format.
  • Output data are returned in XML format.
  • RNAQUA allows to compute the following measures:
    • ClashScore,
    • Root-mean-square deviation (RMSD),
    • Interaction network fidelity (INF),
    • Deformation index (DI),
    • P-value (either for entire RNA 3D structure(s) or for a set of discontinuous 3D substructures).
  • Two processing modes are available:
    • An analysis of single RNA 3D structure (PDB validation, ClashScore, sequence-based analysis, structure unification),
    • An analysis of RNA 3D model(s) with respect to the reference structure (RMSD, INF, DI, P-value, Deformation profile, sequence-based differences between structures, multiple models over the reference structure superposition).
  • Optionally, the user can define alignment between the reference structure and all corresponding RNA 3D model(s) which is helpful if there are differences in sequence, distribution of chains or residue numbering.

This metric tool is maintained by Antczak.

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