A highly accurate method to predict the transcription factors using protein sequences.
TransFacPred is developed for predicting the transcription factors (TFs) using the protein primary sequence information. In this approach, Hybrid model was implemented in which is a combination of ET-based model and BLAST Search. TransFacPred is also available as web-server at https://webs.iiitd.edu.in/raghava/transfacpred. Please read/cite the content about the TransFacPred for complete information including algorithm behind TransFacPred.
PIP version is also available for easy installation and usage of this tool. The following command is required to install the package
pip install transfacpred
To know about the available option for the pip package, type the following command:
transfacpred -h
The Standalone version of transfacpred is written in python3 and following libraries are necessary for the successful run:
Important: NCBI-BLAST version 2.2.29+ is strongly recommended for optimal compatibility with the hybrid model, as it was developed using this specific version. Utilizing a different version may lead to inconsistencies between the outputs obtained from the web server and the standalone application.
To know about the available option for the stanadlone, type the following command:
python transfacpred.py -h
To run the example, type the following command:
python3 transfacpred.py -i protein.fa
This will predict if the submitted sequences are TFs or Non-TFs. It will use other parameters by default. It will save the output in "outfile.csv" in CSV (comma seperated variables).
usage: transfacpred.py [-h]
[-i INPUT
[-o OUTPUT]
[-t THRESHOLD]
[-d {1,2}]
Please provide following arguments for successful run
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input: File name containing protein or peptide sequence in FASTA format.
-o OUTPUT, --output OUTPUT
Output: File for saving results by default outfile.csv
-t THRESHOLD, --threshold THRESHOLD
Threshold: Value between -0.5 to 1.5 by default -0.38
-d {1,2}, --display {1,2}
Display: 1:Transcription Factors, 2: All Sequences, by default 1
Input File: It allow users to provide input in the FASTA format.
Output File: Program will save the results in the CSV format, in case user do not provide output file name, it will be stored in "outfile.csv".
Threshold: User should provide threshold between -0.5 and 1.5.
Patiyal S, Tiwari P, Ghai M, Dhapola A, Dhall A and Raghava GPS (2024) A hybrid approach for predicting transcription factors. Front. Bioinform. 4:1425419.