Astrid, 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 extension). Dr. Guy Plunkett III Senior Scientist Emeritus, UW-Madison Senior Scientist, DNASTAR, Inc. http://www.genome.wisc.edu/information/gplunkett.html On Jun 17, 2017, at 6:00 AM, artemis-users-requ...@sanger.ac.uk<mailto:artemis-users-requ...@sanger.ac.uk> wrote: Send Artemis-users mailing list submissions to artemis-users@sanger.ac.uk<mailto:artemis-users@sanger.ac.uk> To subscribe or unsubscribe via the World Wide Web, visit http://publists.sanger.ac.uk/mailman/listinfo/artemis-users or, via email, send a message with subject or body 'help' to artemis-users-requ...@sanger.ac.uk You can reach the person managing the list at artemis-users-ow...@sanger.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Artemis-users digest..." 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 <a...@sanger.ac.uk> Subject: [Artemis-users] Sequence saved in genbank format does not work in Mauve To: "artemis-users@sanger.ac.uk" <artemis-users@sanger.ac.uk> Message-ID: <afabeda050574c4caed8c33042910ed954722...@exch-mbx1.internal.sanger.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Hi, 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://publists.sanger.ac.uk/mailman/private/artemis-users/attachments/20170616/64f316a7/attachment.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Example_genbank_format.txt URL: <http://publists.sanger.ac.uk/mailman/private/artemis-users/attachments/20170616/64f316a7/attachment-0001.txt> ------------------------------ _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://publists.sanger.ac.uk/mailman/listinfo/artemis-users End of Artemis-users Digest, Vol 16, Issue 1 ********************************************
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