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Single-nucleotide conservation state annotation of SARS-CoV-2 genome.
bioRxiv. 2020 Jul 14B

Abstract

Given the global impact and severity of COVID-19, there is a pressing need for a better understanding of the SARS-CoV-2 genome and mutations. Multi-strain sequence alignments of coronaviruses (CoV) provide important information for interpreting the genome and its variation. We apply a comparative genomics method, ConsHMM, to the multi-strain alignments of CoV to annotate every base of the SARS-CoV-2 genome with conservation states based on sequence alignment patterns among CoV. The learned conservation states show distinct enrichment patterns for genes, protein domains, and other regions of interest. Certain states are strongly enriched or depleted of SARS-CoV-2 mutations, and the state annotations are more predictive than existing genomic annotations in prioritizing bases without non-singleton mutations, which are likely enriched for important genomic bases. We expect the conservation states to be a resource for interpreting the SARS-CoV-2 genome and mutations.

Authors

No affiliation info availableNo affiliation info available

Pub Type(s)

Preprint

Language

eng

PubMed ID

32699851

Citation

Kwon, Soo Bin, and Jason Ernst. "Single-nucleotide Conservation State Annotation of SARS-CoV-2 Genome." BioRxiv : the Preprint Server for Biology, 2020.
Kwon SB, Ernst J. Single-nucleotide conservation state annotation of SARS-CoV-2 genome. bioRxiv. 2020.
Kwon, S. B., & Ernst, J. (2020). Single-nucleotide conservation state annotation of SARS-CoV-2 genome. BioRxiv : the Preprint Server for Biology. https://doi.org/10.1101/2020.07.13.201277
Kwon SB, Ernst J. Single-nucleotide Conservation State Annotation of SARS-CoV-2 Genome. bioRxiv. 2020 Jul 14; PubMed PMID: 32699851.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Single-nucleotide conservation state annotation of SARS-CoV-2 genome. AU - Kwon,Soo Bin, AU - Ernst,Jason, Y1 - 2020/07/14/ PY - 2020/7/24/entrez PY - 2020/7/24/pubmed PY - 2020/7/24/medline JF - bioRxiv : the preprint server for biology JO - bioRxiv N2 - Given the global impact and severity of COVID-19, there is a pressing need for a better understanding of the SARS-CoV-2 genome and mutations. Multi-strain sequence alignments of coronaviruses (CoV) provide important information for interpreting the genome and its variation. We apply a comparative genomics method, ConsHMM, to the multi-strain alignments of CoV to annotate every base of the SARS-CoV-2 genome with conservation states based on sequence alignment patterns among CoV. The learned conservation states show distinct enrichment patterns for genes, protein domains, and other regions of interest. Certain states are strongly enriched or depleted of SARS-CoV-2 mutations, and the state annotations are more predictive than existing genomic annotations in prioritizing bases without non-singleton mutations, which are likely enriched for important genomic bases. We expect the conservation states to be a resource for interpreting the SARS-CoV-2 genome and mutations. UR - https://www.unboundmedicine.com/medline/citation/32699851/Single_nucleotide_conservation_state_annotation_of_SARS_CoV_2_genome_ L2 - https://doi.org/10.1101/2020.07.13.201277 DB - PRIME DP - Unbound Medicine ER -
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