Description

These tracks show curated SARS-CoV-2 protein-coding genes conserved within the Sarbecovirus subgenus as determined using PhyloCSF [1], FRESCo [2], and other comparative genomics methods, consistent with experimental evidence in SARS-CoV-2. Ambiguous gene names were resolved according to the recommendations in [3]. For a complete description of the evidence, see [4].

For a complete description of the evidence, see [4].

Data Access

The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/phyloGenes/PhyloCSFgenes.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Methods

See [4]. Note that the data was updated in June 2021: ORF14 was renamed to ORF9c, ORF2b and ORF3d-2 were added.

Credits

Questions should be directed to Irwin Jungreis.

If you use the SARS-CoV-2 PhyloCSF Genes Track Hub, please cite Jungreis et al. 2021 [4].

References

[1] Lin MF, Jungreis I, and Kellis M (2011). PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Bioinformatics 27:i275-i282 (ISMB/ECCB 2011).

[2] Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC (2015). FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biol. doi: 10.1186/s13059-015-0603-7.

[3] Jungreis, I., Nelson, C. W., Ardern, Z., Finkel, Y., Krogan, N. J., Sato, K., ... & Kellis, M. (2021). Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Virology 558, 145-151. doi.org/10.1016/j.virol.2021.02.013

[4] Jungreis I, Sealfon R, Kellis M (2021). SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nature Communications 12(1), 1-20. doi:10.1038/s41467-021-22905-7