Submitting Genemark annotation to Genbank
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14 months ago
stacy734 ▴ 40

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 • 406 views
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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

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12 months ago
Shalu Jhanwar ▴ 490

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

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