CpG island identification pipeline inspired by the Gardiner-Garden and Frommer (1987) method
Windows and linux grafical user interface standalone programs and a linux command line program are avaliable here:
-
python3.8 or later
-
argparse:
pip3 install argparse
(for the command line script) -
pyfaidx:
pip3 install pyfaidx
-
pandas:
pip3 install pandas
-
Gooey: (for the
gui.py
script)pip install Gooey
With the following script CpG islands are identified by selecting the %GC content, Obs/Exp ratio window and step size. In this example sequence the existence of CpG islands is checked on 200 bp windows with 50 bp interval(the window moves 50bp each time):
python3 cpg_island_identificator.py -in test.fasta -out cpg_table.txt -win 200 -step 50 -gc 55.00
This script can be run also as GUI by running:
python3 cpg_island_identificator_gui.py
and a window will pop up
The output file will look like: