IL5pred

A computational method to predict and scan IL-5 inducing peptides.

Introduction

IL5pred is developed to predict, scan, and design IL-5 inducing peptides. More information on IL5pred web server is available at https://webs.iiitd.edu.in/raghava/il5pred. Please read/cite the content about the IL5pred for complete information including the algorithm behind the approach.

Model

The best Random Forest-based hybrid model (RF(DPC)+BLAST) is implemented in the webserver.

Standalone

Standalone version of IL5pred is written in python3 and the following libraries are necessary for a successful run:

• scikit-learn
• Pandas
• Numpy
• blastp

Minimum usage

To know about the available option for the standalone, type the following command:

python il5pred.py -h

To run the example, type the following command:

python3 il5pred.py -i example_input.fa

This will predict if the submitted sequences are IL-5 inducers or Non-inducers. It will use other parameters by default. It will save the output in "outfile.csv" in CSV (comma-separated variables).

Full Usage:

Following is complete list of all options, you may get these options
usage: il5pred.py [-h] 
                       [-i INPUT]
                       [-o OUTPUT]
		       [-j {1,2,3}]
		       [-t THRESHOLD]
                       [-w {9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}]
		       [-d {1,2}]

Please provide the following arguments

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input: protein or peptide sequence(s) in FASTA format
                        or single sequence per line in a single letter code
  -o OUTPUT, --output OUTPUT
                        Output: File for saving results by default outfile.csv
  -j {1,2,3}, --job {1,2,3}
                        Job Type: 1:Predict, 2: Design, 3:Scan, by default 1
  -t THRESHOLD, --threshold THRESHOLD
                        Threshold: Value between 0 to 1 by default 0.21
  -w {9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}, --winleng {9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}
                        Window Length: 9 to 20 (scan mode only), by default 9
  -d {1,2}, --display {1,2}
                        Display: 1:IL-5 inducing peptides only, 2: All peptides, by default 1

Input File: Allows user to provide input in FASTA format.

Output File: Program will save the results in CSV format, in case the user does not provide the output file name, it will be stored in "outfile.csv".

Threshold: User should provide a threshold between 0 and 1, by default it's 0.21.