Open taltman opened 2 years ago
This is what is desired:
Qualifier /ribosomal_slippage
Definition during protein translation, certain sequences can program
ribosomes to change to an alternative reading frame by a
mechanism known as ribosomal slippage
Value format none
Example /ribosomal_slippage
Comment a join operator,e.g.: [join(486..1784,1787..4810)] should be used
in the CDS spans to indicate the location of ribosomal_slippage
That's actually a different format than the .tbl file that vadr creates, despite them both being (confusingly) called feature tables. The format of vadr output 'feature tables' is described here: https://www.ncbi.nlm.nih.gov/genbank/feature_table/
The vadr format is a useful file format for submissions to GenBank. There may be ways to convert it to a format that ENA accepts for submissions, but I'm not sure what those formats are. The vadr .ftr
output files may also be relatively easy to parse and reformat into an accepted ENA format.
Hi @nawrockie ,
I've so far used VADR to submit nine CoV genomes to ENA with remote homology to SARS-CoV-2. The latest version of DARTH will have the scripts to turn VADR output into a format that can be submitted to ENA using their Webin-CLI tool.
I looked at the GenBank feature_table page, but it doesn't talk about ribosome slippage, and how to encode it correctly (the page seems to be more concerned about syntax). INSDC is a collaboration between GenBank, DDBJ, and EMBL, so why wouldn't the semantics defined for INSDC apply to the GenBank?
VADR outputs the .tbl file format because that was preferred by the GenBank indexers for viral submissions at the time of development. In the GenBank submission pipeline, the vadr .tbl format file is then converted to 'asn' format using tbl2asn
which is used to input the data into the GenBank database.
The latest version of DARTH will have the scripts to turn VADR output into a format that can be submitted to ENA using their Webin-CLI tool.
That sounds good. Have you finished developing the format conversion tool/script, or do you still have a problem with ribosomal_slippage?
VADR produces features with the
/exception
qualifier, to specify ribosomal slippage:But according to the INSDC specs, this is an invalid value:
https://www.insdc.org/documents/feature_table.html#7.3
This causes problems when trying to submit genomes annotated with VADR to ENA.