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