A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
Abstract Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which...
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| Format: | Article |
| Language: | English |
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BMC
2019-05-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2736-2 |
| _version_ | 1818112474734395392 |
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| author | Tao-Chuan Shih Li-Ping Ho Jen-Leih Wu Hsin-Yiu Chou Tun-Wen Pai |
| author_facet | Tao-Chuan Shih Li-Ping Ho Jen-Leih Wu Hsin-Yiu Chou Tun-Wen Pai |
| author_sort | Tao-Chuan Shih |
| collection | DOAJ |
| description | Abstract Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily Results The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily Conclusions Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups. |
| first_indexed | 2024-12-11T03:19:31Z |
| format | Article |
| id | doaj.art-b0c3962805ba42a5bad6825b89d7a89e |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T03:19:31Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b0c3962805ba42a5bad6825b89d7a89e2022-12-22T01:22:40ZengBMCBMC Bioinformatics1471-21052019-05-0120S7495810.1186/s12859-019-2736-2A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae familyTao-Chuan Shih0Li-Ping Ho1Jen-Leih Wu2Hsin-Yiu Chou3Tun-Wen Pai4Department of Computer Science and Engineering, National Taiwan Ocean UniversityCenter of Excellence for the Oceans, National Taiwan Ocean UniversityDepartment of Bioscience and Biotechnology, National Taiwan Ocean UniversityCenter of Excellence for the Oceans, National Taiwan Ocean UniversityDepartment of Computer Science and Engineering, National Taiwan Ocean UniversityAbstract Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily Results The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily Conclusions Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.http://link.springer.com/article/10.1186/s12859-019-2736-2IridoviridaeLinear epitopePropensity scalesHost specificityGroup feature |
| spellingShingle | Tao-Chuan Shih Li-Ping Ho Jen-Leih Wu Hsin-Yiu Chou Tun-Wen Pai A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family BMC Bioinformatics Iridoviridae Linear epitope Propensity scales Host specificity Group feature |
| title | A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family |
| title_full | A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family |
| title_fullStr | A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family |
| title_full_unstemmed | A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family |
| title_short | A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family |
| title_sort | voting mechanism based linear epitope prediction system for the host specific iridoviridae family |
| topic | Iridoviridae Linear epitope Propensity scales Host specificity Group feature |
| url | http://link.springer.com/article/10.1186/s12859-019-2736-2 |
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