I don’t know whether there are any other options in Artemis, but Mauve is 
notoriously picky about the format of “GenBank” files. The example you posted 
looks to be incomplete — no headers at all — so I cannot tell what the issue 
is. It’s been a while since I played this game, but things like 'empty' 
accession and version values in the headers can be enough to cause the problem. 
I posted a bunch of notes to the mauve-users list a few years ago, but ann 
having trouble finding them. If you get stumped, I can take a look at one of 
your files …

The good thing is that once you figure out what is "off" about your file, you 
don't need to rerun the alignment -- since the sequence is unchanged, just 
overwrite the original gbk file with your edited one, and open the alignment in 
Mauve (File: Open Alignment; the output file you open is the one without an 

Dr. Guy Plunkett III
Senior Scientist Emeritus, UW-Madison
Senior Scientist, DNASTAR, Inc.

On Jun 17, 2017, at 6:00 AM,<> 

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Today's Topics:

  1. Sequence saved in genbank format does not work in Mauve
     (Astrid von Mentzer)


Message: 1
Date: Fri, 16 Jun 2017 13:27:33 +0000
From: Astrid von Mentzer <>
Subject: [Artemis-users] Sequence saved in genbank format does not
work in Mauve
To: "" <>

Content-Type: text/plain; charset="iso-8859-1"


I want to use Mauve for a multiple alignment of several genomes. I saved the 
chromsomes in genbank format in Artemis. The alignment works fine in Mauve but 
it can't show the annotations.

Comparing a genbank file from NCBI and the ones generated by Artemis I can see 
many differences but I don't know what is missing and should be changed.
Is there an option to save as "strict genbank" in Artemis?

Anyone who could help me out?

I've attached part of one of my genomes in genbank format.

Best regards,
Astrid von Mentzer
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