Chess2FLYA

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Chemical shift statistics to FLYA


Chess2FLYA is a C++ program that uses RNA secondary structure information in the connectivity table format (.ct file format) and a built-in chemical shift statistics file to generate the following input files for the FLYA automated resonance assignment algorithm implemented in the program package CYANA:

  • CYANA sequence file (.seq) with the RNA sequence
  • XEASY chemical shift list (.prot) with the mean values and standard deviations from 1D shift statistics statistics
  • CYANA torsion angle restraint file (.aco) that restricts the backbone of regular A-form RNA
  • CYANA macro file (.cya) to generate hydrogen bond restraints for the nucleotides involved in regular Watson-Crick base-pairs.

With this input, and peak lists from 2D 1H-1H NOESY, 1H-1H TOCSY, and natural abundance 1H-13C HSQC spectra, the FLYA algorithm can automatically assign the H1', H2, H5, H6, and H8 protons and their corresponding 13C resonances in double-stranded RNA.

Chess2FLYA was developped by Thomas Aeschbacher, Markus Blatter, and Mario Schubert in the group of Prof. Frédéric Allain at ETH Zürich.

Availability

  • Chess2FLYA is freely available. The current version is Chess2FLYA 1.1 (05.04.2015).

Documentation

References

  • Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucl. Acids Res. 41, e172 (2013)
Please cite this paper in reports or publications of results obtained with Chess2FLYA.
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