Actually I think Artemis doesn’t like the location references to another entry, e.g.:
FT gene complement(AC012146.25.1.171309:6053..52695)
Regards
Tim
On 22/6/06 17:21, "Lesley Nicolson" <[EMAIL PROTECTED]> wrote:
Hi – I would really appreciate help with a problem importing files from ensembl export view (http://www.ensembl.org/Homo_sapiens/exportview).
I’ve exported human chromosomal sequence (500Mb) from ensembl export view, with gene, vega and genscan features, as a flat file (saved as text file). In notepad this looks comparable to files that I can open in artemis (apart from the XX blank lines – but it makes no difference removing these): example:
ID 17 standard; DNA; HTG; 500000 BP.
XX
AC chromosome:NCBI36:17:10050467:10550466:1
XX
SV chromosome:NCBI36:17:10050467:10550466:1
XX
DT 21-JUN-2006
XX
DE Homo sapiens chromosome 17 NCBI36 partial sequence 10050467..10550466
DE annotated by Ensembl
XX
KW .
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
On opening the file in artemis, the file is accessed (since I get a base count and reports of trans splicing features) but the sequence does not appear on the artemis screen. I can successfully import sequence into Artemis if I export it as fasta from export view but this means I lose annotation. I have tried saving the feature component of the original file as *.tab file and reading this in once the fasta sequence is loaded but this does not import features into the sequence (annotations are at least partially accessed as I get trans splicing messages but no sequence annotations appear in the sequence screen of artemis). I have also tried importing into vectorNTI and exporting as embl file (whereupon the sequence is accessed but I get a final error message regarding ‘vntifkey not being suitable identifier for source’ and no sequence appears in Artemis (I also get the message vntifkey on readable files prior to sequence appearing in Artemis screen so I don’t think this is related to the loading problem)).
I have tried a sequence a colleague can import into artemis (with success) and he has tried my sequence (and similarly failed) so it does not seem to be a problem peculiar to my installation of artemis/PC environment.
Does anyone have any tricks/workaround/tips I might try ? Many thanks.
Regards,
Lesley Nicolson
Glasgow Veterinary School
Div I&I, Level 4 Sir Henry Wellcome Building
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