PAIVS: prediction of avian influenza virus subtype
Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype caus...
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| Format: | Article |
| Language: | English |
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BioMed Central
2020-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-1-e5.pdf |
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| author | Hyeon-Chun Park Juyoun Shin Sung-Min Cho Shinseok Kang Yeun-Jun Chung Seung-Hyun Jung |
| author_facet | Hyeon-Chun Park Juyoun Shin Sung-Min Cho Shinseok Kang Yeun-Jun Chung Seung-Hyun Jung |
| author_sort | Hyeon-Chun Park |
| collection | DOAJ |
| description | Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users. |
| format | Article |
| id | doaj-art-5b7603730e9c4c8ea5fdb68ee8b44313 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2020-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-5b7603730e9c4c8ea5fdb68ee8b443132025-02-02T21:59:18ZengBioMed CentralGenomics & Informatics2234-07422020-03-0118110.5808/GI.2020.18.1.e5593PAIVS: prediction of avian influenza virus subtypeHyeon-Chun Park0Juyoun Shin1Sung-Min Cho2Shinseok Kang3Yeun-Jun Chung4Seung-Hyun Jung5 Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Chungbuk Veterinary Service Laboratory, Chungju 27336, Korea Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, KoreaHighly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.http://genominfo.org/upload/pdf/gi-2020-18-1-e5.pdfaiv subtypesavian influenza virusnext-generation sequencingviral genome |
| spellingShingle | Hyeon-Chun Park Juyoun Shin Sung-Min Cho Shinseok Kang Yeun-Jun Chung Seung-Hyun Jung PAIVS: prediction of avian influenza virus subtype Genomics & Informatics aiv subtypes avian influenza virus next-generation sequencing viral genome |
| title | PAIVS: prediction of avian influenza virus subtype |
| title_full | PAIVS: prediction of avian influenza virus subtype |
| title_fullStr | PAIVS: prediction of avian influenza virus subtype |
| title_full_unstemmed | PAIVS: prediction of avian influenza virus subtype |
| title_short | PAIVS: prediction of avian influenza virus subtype |
| title_sort | paivs prediction of avian influenza virus subtype |
| topic | aiv subtypes avian influenza virus next-generation sequencing viral genome |
| url | http://genominfo.org/upload/pdf/gi-2020-18-1-e5.pdf |
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