Selected article for: "codon usage percent difference and reference sequence"

Author: Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty
Title: Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
  • Document date: 2020_3_31
  • ID: 2fn25l6m_7
    Snippet: Since the end of last year when it first emerged, SARS-CoV-2 has been mutating and spreading around the world. Ninety-seven complete or near-complete SARS-CoV-2 genomes are currently accessible in GenBank, with various mutations. To determine which SARS-CoV-2 sequence was most appropriate to use, we retrieved all the published sequences of the virus available in GenBank; after excluding incomplete and low-quality sequences, we calculated the perc.....
    Document: Since the end of last year when it first emerged, SARS-CoV-2 has been mutating and spreading around the world. Ninety-seven complete or near-complete SARS-CoV-2 genomes are currently accessible in GenBank, with various mutations. To determine which SARS-CoV-2 sequence was most appropriate to use, we retrieved all the published sequences of the virus available in GenBank; after excluding incomplete and low-quality sequences, we calculated the percent difference in codon usage between these and the reference sequence. The average percent difference in codon usage was 0.029%, or ~3 codons / 10,000, clearly showing that variation in sequences is not significantly affecting overall codon usage. This degree of mutation between strains is corroborated by a recently published study [25] .

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