期刊
RNA
卷 28, 期 3, 页码 277-289出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.078969.121
关键词
subgenomic RNA; SARS-CoV-2; defective viral genomes; user-friendly bioinformatics
资金
- National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur
- ANR (Agence Nationale de la Recherche)
- FRM (Fondation de la Recherche Medicale)
- ANR [ANR-LBX-62 IBEID CoV-2SENSING/COVID 19]
- France Genomique [ANR10-INBS-09-09]
It is crucial to study the production of sgRNA in the vast amount of NGS data of SARS-CoV-2, and a user-friendly bioinformatic tool called sgDI-tector is introduced to identify and quantify these sgRNAs. Researchers successfully detected the nested set of sgRNAs in SARS-CoV-2 using this tool, and compared their production level with other types of viral RNA products.
Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.
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