Method for creating an EMBL formatted annotated sequence?

Question

[Ian]

Does anyone have a method for creating an EMBL-flatfile from a FASTA file of sequence, and a BED file of genes and repeats?

The purpose is for submission of an annotate genome to the ENA.

Thanks.

[Joseph Hughes]

I think this should work. 1) Convert your BED to GFF using GenomeTools: http://genometools.org/tools/gt_bed_to_gff3.html 2) Using seqret from EMBOSS, convert your fasta and gff to embl follwoing this previous post: Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?

Let us know how it goes.

[Sej Modha]

I think Artemis or Sequin can help with that.

Answer 1

[Ian]

Thanks to the other contributors, but unfortunately the EMBL format created was not accepted by ENA. However, I have found EMBLmyGFF3, which will create a valid file.

The validation program can be found HERE.

BED to GFF3 used THIS.

Answer 2

[h.mon]

If you have a ggf3 (or convert your bed to gff3 as suggested by Joseph Hughes), or you can use the tool announced here.