The SARS-CoV-2 genome was annotated using the structured RNA families from the Rfam database including the following Coronavirus-specific families:
The annotations were generated using the
Infernal cmsearch program and the Rfam covariance
models (release 14.2). The cmsearch output was manually edited to remove the lower-scoring
Betacoronavirus-5UTR and Betacoronavirus-3UTR families that belong to the same Rfam clans
as the Sarbecovirus-5UTR and Sarbecovirus-3UTR families (CL00116 and CL00117).
The alignments and the secondary structure were produced using LocARNA and refined based
on the latest literature.
The curated Sarbecovirus alignments were provided by Kevin Lamkiewicz
and Manja Marz
(Friedrich Schiller University Jena). Eric Nawrocki
(NCBI) revised the existing Rfam entries (RF00164, RF00165, and RF00507). We also thank
Ramakanth Madhugiri (Justus Liebig University Giessen) for reviewing the Coronavirus
UTR alignments. The track was prepared by the Rfam team.
This work is part of the BBSRC
funded project to expand the coverage of viral RNAs in Rfam.