A simple python3 implementation of cG/cC score algorithm. cG/cC scoring system is an algorithm proposed by Jean-Denis Beaudoin et al. in 2013 that can be used to characterized the formation capabilities of RNA G-quadruplexes.
The script can be easily executed under the python3 environment (python3.6 is recommended, for that other python versions are not tested).
STEP
s1: Download the source code of cGcC from github.
s2: Execute the python script.
# -i inputfile path
# -o outputfile path
python cGcC.py -i input.txt -o output.txt please note, the input file should contains one column, for each line including one sequence. Below is the example of input file
ACTGCATCACATCAGGGGACTGGGGACACAGGGGACGGGGGACTATCATCACAT
ACAGGGCAGGGCACGGAGGACAGGGACATGCCGGCCC
GAGCCTGGGCACGGGACCACACCATCGGGCACTAGCCACACACAC
GGGCAGGGAGGGAAGGGGAAAGGGGCACGAGGGCGAGCGAGCGAGACA
The script will output two columns into your output file. Column 2 indicates the cGcC score.
ACTGCATCACATCAGGGGACTGGGGACACAGGGGACGGGGGACTATCATCACAT 7.384615384615385
ACAGGGCAGGGCACGGAGGACAGGGACATGCCGGCCC 2.15
GAGCCTGGGCACGGGACCACACCATCGGGCACTAGCCACACACAC 1.2692307692307692
GGGCAGGGAGGGAAGGGGAAAGGGGCACGAGGGCGAGCGAGCGAGACA 12.428571428571429
cGcC citation: Nucleic Acids Res. 2014 Jan;42(2):1209-23. doi: 10.1093/nar/gkt904. Epub 2013 Oct 10.
Bug report: rongxinzhang@seu.edu.cn