Virus Database and Online Inquiry System Based on Natural Vectors
We construct a virus database called VirusDB ( http://yaulab.math.tsinghua.edu.cn/VirusDB/ ) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification info...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2017-12-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/1176934317746667 |
| _version_ | 1818096890312392704 |
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| author | Rui Dong Hui Zheng Kun Tian Shek-Chung Yau Weiguang Mao Wenping Yu Changchuan Yin Chenglong Yu Rong Lucy He Jie Yang Stephen ST Yau |
| author_facet | Rui Dong Hui Zheng Kun Tian Shek-Chung Yau Weiguang Mao Wenping Yu Changchuan Yin Chenglong Yu Rong Lucy He Jie Yang Stephen ST Yau |
| author_sort | Rui Dong |
| collection | DOAJ |
| description | We construct a virus database called VirusDB ( http://yaulab.math.tsinghua.edu.cn/VirusDB/ ) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research. |
| first_indexed | 2024-12-10T23:11:49Z |
| format | Article |
| id | doaj.art-c9f310a576f44792af9d43a75a775eba |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-10T23:11:49Z |
| publishDate | 2017-12-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-c9f310a576f44792af9d43a75a775eba2022-12-22T01:29:56ZengSAGE PublishingEvolutionary Bioinformatics1176-93432017-12-011310.1177/1176934317746667Virus Database and Online Inquiry System Based on Natural VectorsRui Dong0Hui Zheng1Kun Tian2Shek-Chung Yau3Weiguang Mao4Wenping Yu5Changchuan Yin6Chenglong Yu7Rong Lucy He8Jie Yang9Stephen ST Yau10Department of Mathematical Sciences, Tsinghua University, Beijing, ChinaDepartment of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL, USADepartment of Mathematical Sciences, Tsinghua University, Beijing, ChinaInformation Technology Services Center, The Hong Kong University of Science and Technology, Kowloon, Hong KongDepartment of Mathematical Sciences, Tsinghua University, Beijing, ChinaCollege of Computer and Control Engineering, Nankai University, Tianjin, ChinaDepartment of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL, USASchool of Medicine, Flinders University, Adelaide, SA, AustraliaDepartment of Biological Sciences, Chicago State University, Chicago, IL, USADepartment of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL, USADepartment of Mathematical Sciences, Tsinghua University, Beijing, ChinaWe construct a virus database called VirusDB ( http://yaulab.math.tsinghua.edu.cn/VirusDB/ ) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.https://doi.org/10.1177/1176934317746667 |
| spellingShingle | Rui Dong Hui Zheng Kun Tian Shek-Chung Yau Weiguang Mao Wenping Yu Changchuan Yin Chenglong Yu Rong Lucy He Jie Yang Stephen ST Yau Virus Database and Online Inquiry System Based on Natural Vectors Evolutionary Bioinformatics |
| title | Virus Database and Online Inquiry System Based on Natural Vectors |
| title_full | Virus Database and Online Inquiry System Based on Natural Vectors |
| title_fullStr | Virus Database and Online Inquiry System Based on Natural Vectors |
| title_full_unstemmed | Virus Database and Online Inquiry System Based on Natural Vectors |
| title_short | Virus Database and Online Inquiry System Based on Natural Vectors |
| title_sort | virus database and online inquiry system based on natural vectors |
| url | https://doi.org/10.1177/1176934317746667 |
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