PAIVS: prediction of avian influenza virus subtype
| Autor: | Seung-Hyun Jung, Yeun-Jun Chung, Shinseok Kang, Juyoun Shin, Sung-Min Cho, Hyeon-Chun Park |
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| Rok vydání: | 2020 |
| Předmět: |
lcsh:QH426-470
animal diseases Sequence assembly Hemagglutinin (influenza) Health Informatics avian influenza virus medicine.disease_cause Genome DNA sequencing 03 medical and health sciences 0302 clinical medicine Application Note Genetics medicine Ecology Evolution Behavior and Systematics 030304 developmental biology AIV subtypes 0303 health sciences Avian influenza virus biology viral genome virus diseases Pathogenicity Virology Influenza A virus subtype H5N1 Subtyping lcsh:Genetics 030220 oncology & carcinogenesis biology.protein next-generation sequencing |
| Zdroj: | Genomics & Informatics Genomics & Informatics, Vol 18, Iss 1 (2020) |
| ISSN: | 1598-866X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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