EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes
Epitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as ABCPred , SVMTrip , Ep...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2022-05-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322221095221 |
| _version_ | 1818007969033355264 |
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| author | Renato Simões Moreira Vilmar Benetti Filho Nathália Anderson Calomeno Glauber Wagner Luiz Claudio Miletti |
| author_facet | Renato Simões Moreira Vilmar Benetti Filho Nathália Anderson Calomeno Glauber Wagner Luiz Claudio Miletti |
| author_sort | Renato Simões Moreira |
| collection | DOAJ |
| description | Epitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as ABCPred , SVMTrip , EpiDope , and EpitopeVec ; a well-known BCE predictor is BepiPred-2.0. However, despite the prediction, there are several essential steps, such as epitope assembly, evaluation, and searching for epitopes in other proteomes. Here, we present EpiBuilder ( https://epibuilder.sourceforge.io ), a user friendly software that assists in epitope assembly, classifying and searching using input results of BepiPred-2.0. EpiBuilder generates several output results from these data and supports a proteome-wide processing approach. In addition, this software provides the following features: Chou & Fasman beta-turn prediction, Emini surface accessibility prediction, Karplus and Schulz flexibility prediction, Kolaskar and Tongaonkar antigenicity, Parker hydrophilicity prediction, N -glycosylation domains, and hydropathy. These information generate a unique topology for each epitope, visually demonstrating its characteristics. The software can search the entire epitope sequence in various FASTA files, and it allows to use BLASTP to identify epitopes that eventually have sequence variations. As an EpiBuilder application, we developed a epitope dataset from the protozoan Trypanosoma brucei gambiense , the gram-positive bacterium Clostridioides difficile , and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). |
| first_indexed | 2024-04-14T05:22:37Z |
| format | Article |
| id | doaj.art-8fe3f7ae50374dbdbd32391f67cc219c |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-04-14T05:22:37Z |
| publishDate | 2022-05-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-8fe3f7ae50374dbdbd32391f67cc219c2022-12-22T02:10:08ZengSAGE PublishingBioinformatics and Biology Insights1177-93222022-05-011610.1177/11779322221095221EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell EpitopesRenato Simões Moreira0Vilmar Benetti Filho1Nathália Anderson Calomeno2Glauber Wagner3Luiz Claudio Miletti4Instituto Federal de Santa Catarina (IFSC), Lages, BrazilLaboratório de Bioinformática, Universidade Federal de Santa Catarina, Florianópolis, BrazilLaboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, BrazilLaboratório de Bioinformática, Universidade Federal de Santa Catarina, Florianópolis, BrazilLaboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, BrazilEpitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as ABCPred , SVMTrip , EpiDope , and EpitopeVec ; a well-known BCE predictor is BepiPred-2.0. However, despite the prediction, there are several essential steps, such as epitope assembly, evaluation, and searching for epitopes in other proteomes. Here, we present EpiBuilder ( https://epibuilder.sourceforge.io ), a user friendly software that assists in epitope assembly, classifying and searching using input results of BepiPred-2.0. EpiBuilder generates several output results from these data and supports a proteome-wide processing approach. In addition, this software provides the following features: Chou & Fasman beta-turn prediction, Emini surface accessibility prediction, Karplus and Schulz flexibility prediction, Kolaskar and Tongaonkar antigenicity, Parker hydrophilicity prediction, N -glycosylation domains, and hydropathy. These information generate a unique topology for each epitope, visually demonstrating its characteristics. The software can search the entire epitope sequence in various FASTA files, and it allows to use BLASTP to identify epitopes that eventually have sequence variations. As an EpiBuilder application, we developed a epitope dataset from the protozoan Trypanosoma brucei gambiense , the gram-positive bacterium Clostridioides difficile , and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).https://doi.org/10.1177/11779322221095221 |
| spellingShingle | Renato Simões Moreira Vilmar Benetti Filho Nathália Anderson Calomeno Glauber Wagner Luiz Claudio Miletti EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes Bioinformatics and Biology Insights |
| title | EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes |
| title_full | EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes |
| title_fullStr | EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes |
| title_full_unstemmed | EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes |
| title_short | EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes |
| title_sort | epibuilder a tool for assembling searching and classifying b cell epitopes |
| url | https://doi.org/10.1177/11779322221095221 |
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