sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.
SARS-CoV-2
defective viral genomes
subgenomic RNA
user-friendly bioinformatics
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
03 2022
03 2022
Historique:
received:
30
08
2021
accepted:
07
12
2021
pubmed:
24
12
2021
medline:
25
2
2022
entrez:
23
12
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34937774
pii: rna.078969.121
doi: 10.1261/rna.078969.121
pmc: PMC8848934
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
277-289Subventions
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Informations de copyright
© 2022 Di Gioacchino et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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