Selected article for: "coronavirus sequence and envelope protein"
Author: Wang, Shiliang; Sundaram, Jaideep P; Spiro, David
Title: VIGOR, an annotation program for small viral genomes
  • Document date: 2010_9_7
    • ID: 0lbxvudt_45
    Snippet: The gene predictions from two SARS coronavirus genomes (NC_009695 and AY485277) are detailed in Table 3 . NC_009695 is the genomic sequence of a bat SARSlike coronavirus published in 2005 [26] . The annotations have been updated several times by different annotators. This genome encodes 14 ORFs in GenBank. VIGOR predicted 13 ORFs and detected one mutation which resulted in a truncated non-functional peptide ( Table 3 ). The 13 predicted ORFs wer.....
    Document: The gene predictions from two SARS coronavirus genomes (NC_009695 and AY485277) are detailed in Table 3 . NC_009695 is the genomic sequence of a bat SARSlike coronavirus published in 2005 [26] . The annotations have been updated several times by different annotators. This genome encodes 14 ORFs in GenBank. VIGOR predicted 13 ORFs and detected one mutation which resulted in a truncated non-functional peptide ( Table 3 ). The 13 predicted ORFs were exactly the same as the annotations in GenBank. The mutation detected by VIGOR is located in orf3b and generates an internal stop codon, creating truncated peptide of 114 amino acids. The orf3b gene in other coronaviruses is~154 aa long. We believe this truncated protein is non-functional. ZCURVE_V identified 11 ORFs but missed the two short ORFs (28094-28387, 28544-28756) which are completely embedded in the coding region of the nucleocapsid protein. GeneMarkS detected 8 ORFs but ignored 3 additional ORFs. One was the envelope protein gene (26056-26286), and the other two were non-structural protein genes (27573-27707, 27713-28082). Both GeneMarkS and ZCURVE_V did not predict the orf1ab correctly.

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