Method for creating an EMBL formatted annotated sequence?
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.
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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.
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If you have a ggf3 (or convert your bed to gff3 as suggested by Joseph Hughes), or you can use the tool announced here.
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I think Artemis or Sequin can help with that.
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.