il6pred

##A method for predicting and designing IL-6 inducing peptides.

Introduction

IL6Pred is developed for predicting, designing and scanning interleukin-6 inducing peptides. Please read and cite the following paper for complete information including algorithm behind il6Pred.

Models: In this program, one model has been incorporated for predicting interleukin-6 inducing peptides. The model is trained on IL-6 inducing and non-inducing peptides.

Modules/Jobs: This program implement three modules (job types); i) Predict: for predicting interleukin-6 inducing peptides, ii) Design: for generating all possible peptides and computing interleukin-6 inducing potential (score) of peptides, iii) Scan: for creating all possible overlapping peptides of given length (window) and computing interleukin-6 inducing potential (score) of these overlapping peptides.

Reference

Dhall A, Patiyal S, Sharma N, Usmani SS, Raghava GPS (2020) Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19. Brief Bioinform. 22(2):936-945 .

Web Server

https://webs.iiitd.edu.in/raghava/il6pred/

How to install the package, type the following command

pip install il6pred

Minimum USAGE

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

il6pred -h

il6pred -i peptide.fa
``

This will predict the interleukin-6 inducing potential of sequence in fasta format. It will use other parameters by default. It will save output in "outfile.csv" in CSV (comma separated variables).

**Full Usage:** Following is complete list of all options, 

```bash

il6pred  [-h] -i INPUT [-o OUTPUT] [-j {1,2,3}] [-t THRESHOLD]
                  [-w {5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}]
                  [-d {1,2}]


optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input: protein or peptide sequence in FASTA format or single sequence per line in 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 and 3:scan, by default 1
  -t THRESHOLD, --threshold THRESHOLD
                        Threshold: Value between 0 to 1 by default 0.11
  -w {5,6,7,..,25}, --winleng
                        Window Length: 5 to 25 (scan mode only), by default 10
  -d {1,2}, --display {1,2}
                        Display: 1:Interleukin-6 inducing peptide, 2: All peptides, by defaIL6Pred

Input File: It allow users to provide input in two format; i) FASTA format (standard) and ii) Simple Format. In case of simple format, file should have one one peptide sequence in a single line in single letter code (eg. peptide.seq). Please note in case of predict and design module (job) length of peptide should be upto 25 amino acids, if more than 25, program will take first 25 residues. In case of scan module, minimum length of protein/peptide sequence should be more than equal to window length (pattern), see peptide.fa . Please note program will ignore peptides having length less than 8 residues (e.g., protein.fa).

Output File: Program will save result in 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 and 1, please note score is propotional to interleukin-6 inducing potential of peptide.

Address for contact

In case of any query please contact

Prof. G. P. S. Raghava, Head Department of Computational Biology,            
Indraprastha Institute of Information Technology (IIIT), 
Okhla Phase III, New Delhi 110020 ; Phone:+91-11-26907444; 
Email: raghava@iiitd.ac.in  Web: http://webs.iiitd.edu.in/raghava/