ToxinPred2 is an updated version of our server ToxinPred, developed in 2013. It is developed for predicting, mapping and scanning toxic peptides. More information on ToxinPred2 is available from its web server http://webs.iiitd.edu.in/raghava/toxinpred2. This page provide information about standalone version of ToxinPred2. Please read/cite following paper for complete information including algorithm behind ToxinPred2.
Models: In this program, two models have been incorporated;
i) Model1 for predicting given input protein sequence as toxic and non-toxic proteins using Random Forest based on amino-acid composition of the proteins;
ii) Model2 for predicting given input protein sequence as toxic and non-toxic proteins using Hybrid approach, which is the ensemble of Random Forest+ BLAST+ MERCI. It combines the scores generated from machine learning (RF), MERCI, and BLAST as Hybrid Score, and the prediction is based on Hybrid Score.
Modules/Jobs: This program implements three modules; i) Prediction: It allows users to submit multiple sequences in FASTA format, server will predict toxic and non-toxic proteins from their primary sequence. ii) Motif Scan: It allows users to scan or map motifs in the query sequence using MERCI. Here, the user can search for the crucial motifs present in the query protein sequence to find out its role as toxic or non-toxic. iii) BLAST Search: It allows users to search the query protein sequence against the database of known toxic and non-toxic peptides using similarity-based search method.
Minimum USAGE: Minimum usage is "toxinpred2.py -i protein.fa" where peptide.fa is a input FASTA file. This will predict toxic proteins 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, you may get these options by "toxinpred2.py -h".
usage: toxinpred2.py [-h] -i INPUT [-o OUTPUT] [-t THRESHOLD] [-m {1,2}] [-d {1,2}]
Please provide following arguments
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT (Input: protein 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)
-t THRESHOLD, --threshold THRESHOLD (Threshold: Value between 0 to 1 by default 0.6)
-m {1,2}, -- model Model (Model: 1: AAC based RF, 2: Hybrid, by default 1)
-d {1,2}, --display {1,2} (Display: 1:Toxic proteins, 2: All proteins, by default 1)