That is what happened to me using union (and I did use "-feature"):   the
features were incorrectly mapped.    I was using EMBOSS v6.5.7.  Thanks for
the tip on ugene.

The alternative way I got this to work in Artemis was basically as Tim
described,  which was to load an assembly sequence (multifasta) entry  + a
gff file entry. I could then write it back out as an .embl file with the
coordinates remapped to the concatenated assembly.  The process of loading
the gff  (which I downloaded from EupathDB) into Artemis involved a lot of
trial and error and massaging of the GFF file. I also had to edit the final
embl file feature table in order to get gene IDs and products displayed

On Tue, Feb 25, 2014 at 10:31 AM, Bruno Donzelli <> wrote:

>  There was a bug introduced in the later versions  of the "union" routine
> in EMBOSS and I am not sure if it was fixed. As far as I know union may
> work with GFF files but messes up the location of the features in
> concatenated genbank and embl files. I reported the bug almost 2 years ago.
> I have to use the emboss version 6.3.1 to concatenate files correctly.
> Another program that can be used to join files is ugene.Go to workflow
> designer/samples/merge sequences and shift corresponding annotation. Select
> the correct files for input and output. Occasionally this program will
> introduce 2 quotes ("") in place of one (").  Just search and replace using
> a text editor.
> Bruno
> On 25/02/14 04:51, Tim Carver wrote:
> In Artemis, with a multi-fasta sequence file, the options for the
> annotation file are to use a GFF file or to in some way to concatenate the
> EMBL/GenBank feature table (adjusting the coordinates to match the correct
> position of the assembly). This is what 'union' should do with EMBL files.
> I am not sure why this wasn't successful for you.  You obviously do need to
> use '-feature' with union to get the feature table included:
> union -feature -osf embl  entry.embl
> Using GFF and union are the options used here.
> Regards
> Tim
> On 24/02/2014 20:05, "Steven Sullivan" <> wrote:
>  ENA (EMBL) provides TEXT and FASTA file downloads for eukaryotic
> assemblies.  The FASTA download is single a multi-fasta file containing
> separate records for each chromosome. The TEXT download is a single EMBL
> feature table concatenating all the feature tables of the individual
> chromosomes.  It does not contain the DNA sequence.
> Loading these two files into Artemis yields a view of the entire assembly
> as a concatenated sequence, but only the features for the first chromosome
> in the feature file are loaded.
> I understand that this issue has been brought up before. (e.g.
>  What I don't see is a workaround.  Mention was made of the EMBOSS 'union'
> command, which I have tried,  but I  am unable to make that generate an
> .embl file that contains the correctly remapped coordinates of the features
> onto the concatenated sequence. The closest I came to success was an .embl
> file that mapped the first chromosome features only , and incorrectly, onto
> the concatenated sequence.
> Is there a 'correct' way to do load a multifasta record and its annotation
> into Artemis?  The Artemis user manual is rather opaque on this topic.
> _______________________________________________
> Artemis-users mailing 
> --
> Bruno Donzelli
> Research Associate
> Dept. of Plant Pathology and Plant-Microbe Biology, Cornell University
> Robert W. Holley Center for Agriculture and Health
> 538 Tower Road, Cornell University
> Ithaca, NY 14853
> Phone: 607 255-2179

Dr. Steven Sullivan
Center for Genomics & Systems Biology
New York University
12 Waverly Place
New York, NY 10003
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