sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

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-C...

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Detalles Bibliográficos
Autores principales: Di Gioacchino, Andrea, Legendre, Rachel, Rahou, Yannis, Najburg, Valérie, Charneau, Pierre, Greenbaum, Benjamin D., Tangy, Frédéric, van der Werf, Sylvie, Cocco, Simona, Komarova, Anastassia V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2022
Materias:
Bioinformatics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848934/
https://www.ncbi.nlm.nih.gov/pubmed/34937774
http://dx.doi.org/10.1261/rna.078969.121
Descripción
Sumario: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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