RNA Probabilistic Assignment of Imino Resonance Shifts
RNA-PAIRS is part of a multi-step collaborative project aimed at automating RNA chemical shift assignments and structure determination. The first step here is an automated tool for the probabilistic assignment of RNA imino proton resonances and validation of secondary structure.
The beta version provided here accepts as input the user's initial guess of the RNA secondary structure, as well as peak lists from 2D 1H-15N HSQC and 2D 1H-1H exchangeable NOESY spectra.
Acceptable formats for input data are:
- 1H-15N HSQC and 2D 1H-1H exchangeable NOESY peak lists in Sparky format. Peak lists can cover whole spectra or only the imino region; however we have found that full-spectrum peak lists for 2D 1H-1H exchangeable NOESY increase assignment accuracies.
- Secondary structure of the RNA in PAIRS format.
The output is a ranked list of assignment probabilities for resonances within the range expected for imino protons (9-15 ppm), and a prescribed RNA secondary structure most consistent with submitted data and predictions from thermodynamic parameters (Turner's Rules).
Assignment probabilities, prescribed secondary structure, and other outputs are returned via email. If you fail to receive an email in a few minutes, please contact NMRFAM Software Development Team (firstname.lastname@example.org).
A full description of RNA-PAIRS input and output files can be found here.
The current version or RNA-PAIRS is under development and should be used with caution. We will continue debugging and updating our algorithm until a final version is available. Comments are welcome and appreciated to improve RNA-PAIRS.
|Arash Bahrami (U.Wisc)
|Lawrence J. Clos II (U.Wisc)
|Hamid R. Eghbalnia (U.Cinn)
|Samuel E. Butcher (U.Wisc)
|John L. Markley (U.Wisc)
A service offered by the National Magnetic Resonance Facility at Madison. Updated DECEMBER 2011.