Description
The ability to predict B cell epitopes from antigen sequences is critical for biomedical research and many clinical applications. However, despite substantial efforts over the past 20 years, the performance of even the best B cell epitope prediction software is still modest. Based on the idea of T-B reciprocity, BepiTBR is a B cell epitope prediction model that demonstrates improved performance by incorporating prediction of nearby CD4+ T cell epitopes close to the B cell epitopes.
Fasta Mode identifies potential B cell epitopes from a .fasta file containing multiple antigen protein sequences. This mode requires protein sequence file in fasta format.
Usage
Example command using provided example files:
(replace paths with appropriate paths according to user's particular installation)
raku BepiTBR.raku \--fasta0=examples/test_data_BepiTBR_fasta/peptide_with_full_length.txt \--length=15 \--bepipred2=bp2/bin/activate \--bepipred1=/home/exampleUser/bp1/bepipred-1.0/bepipred \--LBEEP=/home/exampleUser/LBEEP/ \--MixMHC2pred=/home/exampleUser/MixMHC2pred/MixMHC2pred_unix \--netMHCIIpan=NA \--dir=/home/exampleUser/BepiTBR/examples/test_output_BepiTBR \--thread=4
Arguments
| Name | Explanation | |
|---|---|---|
| fasta0 | protein sequence file in fasta format | |
| length | length of the B cell epitopes to scan in a moving window. Recommended length: 15 | |
| bepipred2 | the conda environment activation file for BepiPred 2.0 | |
| bepipred1 | path to the BepiPred 1.0 executable | |
| LBEEP | path to the LBEEP directory | |
| MixMHC2pred | path to the MixMHC2pred executable. | |
| netMHCIIpan | path to the NetMHCIIpan 3.2 executable | |
| dir | output directory | |
| thread | number of CPU thread to use; system dependent | |
Details
1. Required tools (BepiPred 1.0, BepiPred 2.0, LBEEP 1.0, NetMHCIIpan 3.2, MixMHC2pred) must be installed before executing model. For more details about installation and other dependencies, please visit our GitHub.
2. For BepiPred 2.0, this tool requires an isolated python virtual environment (python 2.7). After installation, It is recommended to move the bp2 env directory into the BepiTBR main directory.
3. It is recommended to set netMHCIIpan to NA for better run speed.