VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki

In our tests of the NC and DC datasets, VAPiD failed 43 total sequences; 12 of these were also failed by VADR and 31 were passed by VADR and VIGOR (Table 7) . Of the 12, nine had an internal stop (SEQ FEAT.InternalStop) or another CDS translation problem (SEQ FEAT.CdsTransFail), one had a start codon problem (SEQ FEAT.StartCodon), one was reverse complemented (FV536857.1; this was the only sequence of the 12 that failed VIGOR as well), and one failed because no similar reference was found for it. All 31 sequences that failed VAPiD but did not fail the other two programs (30 from the NC set and 1 from the DC set) were either 5' truncated in the first CDS (Norovirus nonstructural polyprotein or Dengue virus polyprotein) or 3' truncated in the final CDS (Norovirus VP2) or both, according to the VADR and VIGOR results, but were otherwise valid. These all failed VAPiD with at least one of the SEQ FEAT.NoStop or SEQ FEAT.CdTransFail This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.