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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Sun Aug 14 04:32:46 EDT 2011


> 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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