A tool for predicting and scanning the peptides with the ability to bind non-classical class-I HLA alleles
Project description
HLAncPred
Introduction
HLAncPred is developed for predicting and scanning the peptides with the ability to bind non-classical class-I HLA alleles such as HLA-G*01:01,HLA-G*01:03,HLA-G*01:04, HLA-E*01:01, HLA-E*01:03 . More information on HLAncPred is available from its web-server https://webs.iiitd.edu.in/raghava/hlancpred/stand.html. This page provides information about stnadalone version of HLAncPred. Please read/cite the content about the HLAncPred for complete information including algorithm behind HLAncPred.
Models: In this program, five best models devoted to each allele, have been implemented for predicting the non-classical class-I HLA binder peptides. The models were trained on experimentally verified binders and randomly generated non-binders using Swiss-Prot database.
Modules/Jobs: This program implements two modules (job types); i) Predict: for prediction of non-classical class-I HLA allele binder peptides, ii) Scan: for creating all possible overlapping peptides of given length (window) and computing binding potential (score) of the overlapping peptides.
Minimum USAGE: Minimum usage is "python3 hlancpred.py -i peptide.fa -a G0101," where peptide.fa is a input fasta file, and 'G0101' is the name for HLA-G*01:01 against which the binders will be predicted. This will predict the binding ability of sequence in fasta format against HLA-G*01:01. It will use other parameters by default. It will save output in "outfile.csv" in CSV (comma seperated variables).
Full Usage: Following is complete list of all options, you may get these options by "python hlancpred.py -h"
usage: hlancpred [-h] -i INPUT -a {G0101,G0103,G0104,E0101,E0103} [-o OUTPUT] [-j {1,2}] [-w {8,9,10,11,12,13,14,15}] [-d {1,2}]
Please provide following arguments
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
-a {G0101,G0103,G0104,E0101,E0103}, --allele {G0101,G0103,G0104,E0101,E0103}
Please provide the name of allele for the prediction of binder peptides
-o OUTPUT, --output OUTPUT
Output: File for saving results by default outfile.csv
-j {1,2}, --job {1,2}
Job Type: 1:predict, and 2:scan, by default 1
-w {8,9,10,11,12,13,14,15}, --winleng {8,9,10,11,12,13,14,15}
Window Length: 8 to 35 (scan mode only), by default 9
-d {1,2}, --display {1,2}
Display: 1:Only binders, 2: All peptides, by default 1
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 peptide sequence in a single line in single letter code (eg. peptide.seq). Note: 1: In case of predict and design module (job), the length of peptide should be upto 15 amino acids. If a sequence with length more than 15 will be provided, the program will take first 15 residues, and ignore the rest. In case of scan module, minimum length of protein/peptide sequence should be equal to window length (pattern), see peptide.fa. 2: Program will ignore peptides having length less than 8 residues (e.g., protein.fa).
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".
Allele: The program needs the name of the allele as shown in the usage, it could be G0101, G0103, G0104, E0101, and E0103.
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