circTIS is a computational tool designed to translation initiation sites (TIS) prediction in circRNAs.
Repository of circTIS development: https://github.com/denilsonfbar/circTIS-exps-BSB2023
Clone the circTIS repository:
git clone https://github.com/denilsonfbar/circTIS.git
Enter the circTIS folder:
cd circTIS
Create Conda environment from environment.yml configuration file:
conda env create -f environment.yml
Activate the created environment:
conda activate circtis_env
Run the prediction example using Python interpreter:
python3 circtis.py -f example/circRNA_seqs.fa
OR
Give execution privileges to the circCodAn script file:
chmod +x circtis.py
And run the example directly from the script file:
./circtis.py -f example/circRNA_seqs.fa
OR
If you need to run circTIS from anywhere on the file system, update the PATH variable:
export PATH=$PATH:path/to/circTIS
And run the example from anywhere on the file system:
circtis.py -f path/to/example/circRNA_seqs.fa
2023-05-31 15:48:48 -> started circTIS v1.0
2023-05-31 15:49:01 -> prediction finished
Number of input sequences -> 100
Number of predicted TIS -> 92
All possible TIS file -> example/circTIS_output/all_possible_TIS.tsv
Predicted TIS file -> example/circTIS_output/predicted_TIS.tsv
The files with the outputs of circTIS execution are recorded at the addresses given.
Install the following requirements:
Carry out of the same steps described in Installation section, except for creating and activating the Conda environment.
Usage: circtis.py [options]
Options:
-h, --help show this help message and exit
-f file, --file=file mandatory - input circRNAs file (FASTA format). Ex:
example/circRNA_seqs.fa
-t string, --tis=string
optional - TIS types for search. Options:
ATG
NC1 [ATG, CTG, GTG, TTG]
NC2 [ATG, CTG, GTG, TTG, AAG, ACG, AGG, ATA, ATC, ATT]
[default = NC1]
-o folder, --output=folder
optional - path to output folder. Ex:
path/to/output_folder
if not declared, it will be created at the circRNAs
input folder
[default = "circTIS_output"]
Basic example to find TIS in circRNA sequences:
python3 circTIS.py -f example/circRNA_seqs.fa
If you use or discuss circTIS, please cite:
Barbosa, D.F., Oliveira, L.S., Kashiwabara, A.Y. (2023). circTIS: A Weighted Degree String Kernel with Support Vector Machine Tool for Translation Initiation Sites Prediction in circRNA. In: Reis, M.S., de Melo-Minardi, R.C. (eds) Advances in Bioinformatics and Computational Biology. BSB 2023. Lecture Notes in Computer Science, vol 13954. Springer, Cham. https://doi.org/10.1007/978-3-031-42715-2_2
To report bugs, to ask for help and to give any feedback, please contact [email protected]