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vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data.
Cai, Zena; Fu, Ping; Qiu, Ye; Wu, Aiping; Zhang, Gaihua; Wang, Yirong; Jiang, Taijiao; Ge, Xing-Yi; Zhu, Haizhen; Peng, Yousong.
Afiliación
  • Cai Z; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
  • Fu P; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
  • Qiu Y; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
  • Wu A; Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
  • Zhang G; Suzhou Institute of Systems Medicine, Suzhou, China.
  • Wang Y; The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
  • Jiang T; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
  • Ge XY; Guangzhou Laboratory, Guangzhou, China.
  • Zhu H; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
  • Peng Y; Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
Brief Bioinform ; 23(6)2022 11 19.
Article en En | MEDLINE | ID: mdl-36377755
Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: MicroARNs Límite: Animals Idioma: En Revista: Brief Bioinform Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2022 Tipo del documento: Article País de afiliación: China

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: MicroARNs Límite: Animals Idioma: En Revista: Brief Bioinform Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2022 Tipo del documento: Article País de afiliación: China