[Bioperl-l] Genbank file : bad features (tag) order with /translation

Chris Fields cjfields at illinois.edu
Sun Aug 14 10:22:10 EDT 2011


Not that I'm aware of, though it shouldn't be hard to set something up using Bio::SeqIO for that.

chris

On Aug 14, 2011, at 3:32 AM, Torsten Seemann wrote:

>> I currently use BioPerl and SeqIO::genbank to create the *gbf files for NCBI submission, they've always accepted them. In fact I think they don't even use them, I believe they use the *tbl, *fsa, and *agp files and the ASN file as data sources.
> 
> I'm pretty sure that NCBI/Genbank do *not* accept Genbank files for
> submission - which I found somewhat ironic!
> 
> They require an ASN1 formatted file (XML-like hierarchial format,
> pre-dates XML), which is sometimes given a .sqn extenison if you use
> the Sequin GUI to prepare it. There are command line tools like
> "tbl2asn" which will take the .tbl and .fsa files Brian has listed to
> produce the ASN file too.
> 
> As far as I know, there is no NCBI tools to take a .gbk and produce
> the .tbl/.fsa/.agp - does anyone know otherwise?
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
> University, AUSTRALIA
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