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postgraduate thesis: PRRSV-webtool: a web-based database and phylogenetic tool to study molecular epidemiology and evolution ofporcine reproductive and respiratory syndrome virus, and related tooland algorithm

TitlePRRSV-webtool: a web-based database and phylogenetic tool to study molecular epidemiology and evolution ofporcine reproductive and respiratory syndrome virus, and related tooland algorithm
Authors
Issue Date2013
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Wong, L. C. [王禮賢]. (2013). PRRSV-webtool : a web-based database and phylogenetic tool to study molecular epidemiology and evolution of porcine reproductive and respiratory syndrome virus, and related tool and algorithm. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5053426
AbstractPorcine Reproductive and Respiratory Syndrome virus (PRRSV) causes the disease - Porcine Reproductive and Respiratory Syndrome (PRRS) which is one of the most economically important diseases for pig farmers. Since it was discovered in the United States and Europe, it has quickly affected the swine industry all over the world. Studying and controlling PRRSV has become an important issue in swine industry and scientific community, and has raised the concerns of governments like US and China. By using different bioinformatics and phylogenetics tools, scientists could understand the epidemiology and evolution of PRRSV from genomic data. However, a well-designed database for PRRSV sequence and relevant meta-information are generally required for the tools to produce insightful results. Therefore, I would like to introduce an easily accessible web platform for PRRSV analysis - PRRSV-Webtool. The core component of PRRSV-Webtool is phylogenetic reconstruction. Instead of using traditional phylogenetic reconstruction, a new method of reconstruction was introduced - Reconstruction by Addition of Taxon (RAT). RAT could build a phylogenetic tree from known existing phylogeny. Simulation tests were performed to evaluate the accuracies of RAT using PRRSV dataset. The percentages of correct branch reconstruction are 73.81% for type 1 PRRSV dataset and 80.68% for type 2 PRRSV dataset. Another important function of PRRSV-Webtool is genotyping. RAT could correctly identify the genotype of all sequences in the testing datasets. PRRSV-Webtool combined three main components: database, phylogenetic tool and World Wide Web. By using PRRSV-Webtool, the users can study their own PRRSV genome data easily via the web browser. Tools in PRRSV-Webtool can allow users to know more about their PRRSV isolates related to other field samples. With our PRRSV-Webtool, scientists and veterinaries can help to improve their understanding of PRRSV and help to control the virus by accelerating the process of virus surveillance and field sampling.
DegreeMaster of Philosophy
SubjectPorcine reproductive and respiratory syndrome - Epidemiology.
Viruses - Phylogeny.
Swine - Virus diseases.
Dept/ProgramBiological Sciences
Persistent Identifierhttp://hdl.handle.net/10722/188307

 

DC FieldValueLanguage
dc.contributor.authorWong, Lai-yin, Charles.-
dc.contributor.author王禮賢.-
dc.date.accessioned2013-08-27T08:03:34Z-
dc.date.available2013-08-27T08:03:34Z-
dc.date.issued2013-
dc.identifier.citationWong, L. C. [王禮賢]. (2013). PRRSV-webtool : a web-based database and phylogenetic tool to study molecular epidemiology and evolution of porcine reproductive and respiratory syndrome virus, and related tool and algorithm. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5053426-
dc.identifier.urihttp://hdl.handle.net/10722/188307-
dc.description.abstractPorcine Reproductive and Respiratory Syndrome virus (PRRSV) causes the disease - Porcine Reproductive and Respiratory Syndrome (PRRS) which is one of the most economically important diseases for pig farmers. Since it was discovered in the United States and Europe, it has quickly affected the swine industry all over the world. Studying and controlling PRRSV has become an important issue in swine industry and scientific community, and has raised the concerns of governments like US and China. By using different bioinformatics and phylogenetics tools, scientists could understand the epidemiology and evolution of PRRSV from genomic data. However, a well-designed database for PRRSV sequence and relevant meta-information are generally required for the tools to produce insightful results. Therefore, I would like to introduce an easily accessible web platform for PRRSV analysis - PRRSV-Webtool. The core component of PRRSV-Webtool is phylogenetic reconstruction. Instead of using traditional phylogenetic reconstruction, a new method of reconstruction was introduced - Reconstruction by Addition of Taxon (RAT). RAT could build a phylogenetic tree from known existing phylogeny. Simulation tests were performed to evaluate the accuracies of RAT using PRRSV dataset. The percentages of correct branch reconstruction are 73.81% for type 1 PRRSV dataset and 80.68% for type 2 PRRSV dataset. Another important function of PRRSV-Webtool is genotyping. RAT could correctly identify the genotype of all sequences in the testing datasets. PRRSV-Webtool combined three main components: database, phylogenetic tool and World Wide Web. By using PRRSV-Webtool, the users can study their own PRRSV genome data easily via the web browser. Tools in PRRSV-Webtool can allow users to know more about their PRRSV isolates related to other field samples. With our PRRSV-Webtool, scientists and veterinaries can help to improve their understanding of PRRSV and help to control the virus by accelerating the process of virus surveillance and field sampling.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.source.urihttp://hub.hku.hk/bib/B50534269-
dc.subject.lcshPorcine reproductive and respiratory syndrome - Epidemiology.-
dc.subject.lcshViruses - Phylogeny.-
dc.subject.lcshSwine - Virus diseases.-
dc.titlePRRSV-webtool: a web-based database and phylogenetic tool to study molecular epidemiology and evolution ofporcine reproductive and respiratory syndrome virus, and related tooland algorithm-
dc.typePG_Thesis-
dc.identifier.hkulb5053426-
dc.description.thesisnameMaster of Philosophy-
dc.description.thesislevelMaster-
dc.description.thesisdisciplineBiological Sciences-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b5053426-
dc.date.hkucongregation2013-

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