This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Submitting Genemark annotation to Genbank

Hi all, I have Genmark-ES output for a plant genome. Genemark output is in gft format and I'm stumped as to how to get it into a format I can submit to Genbank.

Genbank's tbl2asn program requires tbl format annotation. Various programs (GAG, etc) to convert gft to tbl don't seem to work very well as a lot of the information is missing in the tbl file. Genbank table2asn (different than tbl2asn) indicates they can input gft, but it throw a lot of errors about not being able to resolve anything past contig_1.

Has anyone else submitted Genemark-ES output, and how did you do it? Thanks!

genemark genbank genomes
• 1,935 views • link
updated by Shalu Jhanwar Shalu Jhanwar • written by stacy734 • stacy734

does it has to go to Genbank? I mean would submitting it to ENA also be an option?

if so, you could have a look at the EMBLmyGff : GFF3 to EMBL converter

• 0 views • link
written by lieven.sterck lieven.sterck

1 answer

How about EMBOSS (seqret). Have a look at similar Biostar post: Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?

• 0 views • link
written by Shalu Jhanwar Shalu Jhanwar

Log in to answer this question.

More posts like this