iM-Seeker is commandline software designed to predict DNA i-Motif folding status and folding strength.
The dependency packages can be installed by:
pip3 install -r requirements.txt
iM-Seeker (available at https://pypi.org/project/iM-Seeker/) can be installed by:
pip3 install iM-Seeker
Alternatively, the python script 'iM-Seeker.py' can be downloaded directly from Github. The stored directory can be added to the ‘PATH’ environmental variable or the scripts with full path can be run alternatively using command like:
python3 iM-Seeker.py -h
Please pay attention !!!!!! The program needs two models 'pickle_model_classification.pkl' and 'pickle_model_regression.pkl' which are required as the input files of the software. Please find all the files at https://figshare.com/s/e4e72e2e8ceaa0a4fbd6, where all these files can be downloaded directly.
After intalled the package with 'pip',the help page can be checked by following command:
iM-Seeker.py -h
Parameters can be configured according to the user's own needs. Here is an example:
iM-Seeker.py --sequence input.fa --classification_model pickle_model_classification.pkl --regression_model pickle_model_regression.pkl --overlapped 2 --greedy 2 --stem_short 3 --stem_long 5 --loop1_short 1 --loop1_long 12 --loop2_short 1 --loop2_long 12 --loop3_short 1 --loop3_long 12 --representative_conformation 2 --output_folder output_path
The input sequences should be in fasta formation, for instance:
>test1
CCCTCCCCCTCCCCTCCCTCCCCCCCCTCCCCTCCCTCCCTCCCCCCCCTCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCTCCTCCCCTCCCCCTCCCCTCCCTCCCTCC
>test2
CCCCCTCCCCCTCCCCCTCCCCCTCCCCC
>test3
CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
>test4
CCCCGACCCCAACCCCTCCCCCAACCCCTCCCC
The output files are stored in the pre-set output folder.
If --representative_conformation is set as 1, 'iM-seeker_result_average_conformation.txt' includes conformation A of pre-set iM structures.
If --representative_conformation is set as 2, 'iM-seeker_result_side_shorter_conformation.txt' includes conformation B of pre-set iM structures.
The prediction result is kept in 'iM-seeker_final_prediction.txt'.
"0" of folding status means unfolded while "1" means folded. Folding strength is a continuous number.
We provide the 'test.fa' in zipped folder 'test'. 'test.fa' contains Chr4 and Chr5 of Arabidopsis thaliana. Besides, there are two example output files.
After intalled the package with 'pip', the same output files as 'iM-seeker_final_prediction_test.txt', and 'iM-seeker_result_average_conformation_test.txt' can be generated with the following command:
iM-Seeker.py --sequence test.fa --classification_model pickle_model_classification.pkl --regression_model pickle_model_regression.pkl
'pickle_model_classification.pkl' and 'pickle_model_regression.pkl' should be replaced by users' own path.