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 union¹ should do with EMBL files. I am not sure
why this wasn¹t successful for you. You obviously do need to use -feature¹
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> 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.
> https://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00690.html) 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.
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