13Check_RNA

A tool to evaluate ¹³C chemical shifts assignments of RNA

Installing

    0. The Python programming language is a basic requirement. If you don't have it, then install Anaconda or Miniconda.

1. Download and unzip or clone the repository from https://github.com/BIOS-IMASL/13Check_RNA.

2. Execute the following command in your terminal:

pip install 13Check_RNA/

Using the checkrna module

In this Jupyter Notebook you can run the following commands and the examples of use, and check-out the output messages and error-warnings.

0. In a Python script or Jupyter notebook write:

import checkrna

    1.0 To evaluate RNA ¹³C chemical shifts from a new nmrstar file not deposited in the BMRB yet:

checkrna.checkcarbons('path to the new nmrstar file')

       Where 'path to new nmrstar file' is a string.

    Example of use:

checkrna.checkcarbons('example_files/new_nmrstar_file.str')

    1.1 To check for systematic errors in ¹³C chemical shifts of an RNA BMRB entry:

checkrna.checkcarbons(bmrb entry number)

       Where bmrb entry number is an integer.

    Example of use:

checkrna.checkcarbons(15869)

    1.2 To check for systematic errors in RNA ¹³C chemical shifts of a nmrstar file downloaded from the BMRB:

checkrna.checkcarbons('path to nmrstar file')

       Where 'path to nmrstar file' is a string.

    Example of use:

checkrna.checkcarbons('example_files/bmr7403.str')

Types of output messages and error-warnings you may expect:

• If 13C chemical shifts are correct:

checkrna.checkcarbons(4346)

    Nitrogenous base 13C chemical shifts of BMRB id 4346 are correct
    Ribose 13C chemical shifts of BMRB id 4346 are correct

• If 13C chemical shifts have a systematic error:

checkrna.checkcarbons(15869)

    Nitrogenous base 13C chemical shifts of BMRB id 15869 have a systematic error of -2.69ppm
    Ribose 13C chemical shifts of BMRB id 15869 have a systematic error of -2.69ppm

• If part of the 13C chemical shifts are correct but another part has a systematic error:

checkrna.checkcarbons(5932)

    Nitrogenous base 13C chemical shifts of BMRB id 5932 are correct
    Ribose 13C chemical shifts of BMRB id 5932 have a systematic error of -2.59 ppm

    or

checkrna.checkcarbons(xxxx)

    Nitrogenous base 13C chemical shifts of BMRB id xxxx have a systematic error of -2.71 ppm
    Ribose 13C chemical shifts of BMRB id xxxx are correct

• If 13C chemical shifts have non-systematic errors (i.e. random errors):

checkrna.checkcarbons(6239) 

    13C chemical shifts of BMRB id 6239 have non-systematic errors

• If 13C chemical shifts can not by evaluated because the RNA molecule has not enough reference nuclei:

checkrna.checkcarbons(xxxx) 

    BMRB id xxxx has not enough reference nuclei

• If 13C chemical shifts can not by evaluated because the RNA molecule lacks the terminal sequence necessary to apply this method:

checkrna.checkcarbons(7090)

    UserWarning: The method cannot be applied because this RNA molecule has no 5'-GG/3'-C terminal sequence

• If BMRB entry doesn't exist:

checkrna.checkcarbons(919929) 

    OSError: Entry '919929' does not exist in the public database.

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

• We thank Jon Wedell, for helping us with the PyNMRSTAR library

Citation

If you find this module (or the information contained in this repository) useful, please cite us:

A A Icazatti, O A Martin, M Villegas, I Szleifer, J A Vila; 13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA, Bioinformatics, , bty470, https://doi.org/10.1093/bioinformatics/bty470