Don't know if this helps, since it is slightly different to the problem you
mention, but this worked for me to produce a file to look at Bam files mapped
against all 14 Plasmodium chromosomes concatenated in Artemis, sequences +
1. Save files of individual chromosomes in Artemis as embl format
2. Use program yank to make list file of the individual chromosome file names,
3. Do union -sequence @cds.list -sformat embl -outseq Pfall.embl -osformat embl
4. Open Pfall.embl in Artemis
From: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk]
on behalf of Tim Carver [t...@sanger.ac.uk]
Sent: Tuesday, February 25, 2014 4:51 AM
To: Steven Sullivan; firstname.lastname@example.org
Subject: Re: [Artemis-users] loading a eukaryotic genome assembly(multifasta)
and annotation into Artemis 16.0.0
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.
On 24/02/2014 20:05, "Steven Sullivan" <sulli...@nyu.edu<UrlBlockedError.aspx>>
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
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.
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
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.
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