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