LBEEP V1.0

Linear B-Cell Exact Epitope Predictor

1. Introduction

   LBEEP (Linear B-Cell Exact Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell epitopes. Please refer the article tilted "Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-based Feature Descriptor" for more deatils.

2. Installation

   Linux OS (a) Download LBEEP from github. (b) Extract the files to the desired location. (c) Provide executable permission to LBEEP file (if it doesn't have executable rights). (d) Create folder named "temp" and provide read and write permission to "temp" folder. (e) make sure java 1.6 or higher is installed in your system. (f) make sure PERL 5.0 or higher version is installed in your system.

   Windows and other operating system (a) The source code has been writtern in PERL and hence it can be executed as perl script in other operating system. Note: The program is not tested in any other operating system (except Linux based OS) and hence not advised to execute in other OS.

   Using Docker

   1. Build the container docker build -t lbeep .
   2. To test the container is working: docker run -it lbeep -i test_input_peptides -m pep
   • This will work from an input file that exists INSIDE the container and write the output file there as well.
   3. To run with input and output files on the host system, you will need to provide at least one bind mount, e.g.: docker run -v `pwd`:/io -it lbeep -i /io/path_to_input -m pep -o /io/path_to_output_file. Note that the paths beginning with '/io', will be from the perspective of the container, not the host.

3. Command line options

   -i : input file in fasta format (mandatory). Note: The option does not validate the FASTA format and hence make sure the input sequence is in fasta format. -m : mode either 'pep' for peptide or 'pro' for protein (mandatory). -M : Model to be used 'B' for balanced model, 'C' for confirmed model, and 'O' for original model (default Balanced model). For the confirmed model, the dataset constructed in LBtope (LBtope_confirm) was utilizd, where epitopes/non-epitopes were confirmed by atleast two experimental studies. -t : threshold for predcition; integer ranging between 0.0 and 1.0 (default 0.6). -o : output file (if not mentioned output will be stored in LBEEP_out file).

4. Output Interpretation

   (a) A CSV (comma seperated values) file will be generated as output for both peptide and protein mode, which contans serial number, peptideheader|input peptide|, and probability score for the peptide mode and Position of peptide in protein, |peptide|, and probability score for protein mode. (b) In case of protein mode, the program queries the user whether to save the result in HTML format or NOT, if opted yes a HTML file will be saved in the name of filename mentione in -o option with the extension of .html. The result in the html file is self explanatory. (c) The peptides having score greater than threshold mentioned in -t is considered epitopes.

5. Limitations

   (a) Since the models (Original and Balanced) are trained using epitopes and non-epitopes of length >5 and <=15, predictions made for peptides other than these lengths will be undesirable. Hence, it is advised not to mention window size less than 6 and greater than 15 in protein mode, and not advised to input peptides of length less than 6 and greater than 15 in peptide mode. However, these may not be true in the case of "Confirm" mode.

6. Example

   (a) ./LBEEP -i test_input_peptides -m pep -M B -o Test_peptide (b) ./LBEEP -i test_input_protein -m pro -M B -t 0.6 -o Test_protein (c) ./LBEEP -i test_input_peptides -m pep -M C -o Test_peptide_confirm

7. License

   LBEEP V1.0 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation version 3.0 of the License. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License contained in the file LICENSE for more details.

8. Contact: For queries [email protected]; [email protected];