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.
Epitope Mode analyzes specific epitopes within proteins. This mode requires epitope sequences and their corresponding full antigen protein sequences
Usage
Example command using provided example files:
(replace paths with appropriate paths according to user's particular installation)
raku BepiTBR.raku \--motif0_file=examples/test_data_BepiTBR/Ind-positive.txt \--full0_file=examples/test_data_BepiTBR/peptide_with_full_length.txt \--bepipred2=bp2/bin/activate \--bepipred1=/home/exampleUser/bp1/bepipred-1.0/bepipred \--LBEEP=/home/exampleUser/LBEEP/ \--MixMHC2pred=/home/exampleUser/MixMHC2pred/MixMHC2pred_unix \--netMHCIIpan=/home/exampleUser/netMHCIIpan-3.2/netMHCIIpan \--dir=/home/exampleUser/BepiTBR/examples/test_output_BepiTBR \--thread=4
Arguments
| Name | Explanation | |
|---|---|---|
| motif0_file | candidate epitopes file | |
| full0_file | full protein sequences file | |
| 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.