Hi Jack,
A quick solution is to insert a short sequence containing stop codons
in all six reading frames in between every contig sequence in your
fasta file. I agree it would be nice to have this as an artemis feature.
Cheers
Scott
On 26/06/2007, at 1:03 AM, Jack van de Vossenberg wrote:
Dear all,
I am not sure if this came up already, but I have a question. If it
cannot be done I'll make it a feature request.
We have a 454 genome sequence, which is fragmented into many
contigs. We used a fasta file of all contigs to start genome
annotation. Artemis was used to determine ORFs.
Unfortunately some ORFs cross the contig border to the next (random
position) contig. This makes annotation, especially automated
blasts, more difficult, and sometimes we miss info. Is there a way
to tell Artemis not to cross contig borders while defining ORFs? If
it is not possible I request an option for this for future
releases ;) I think that more and more people will have fragmented
genome data for quick/early screening.
Cheers, Jack
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---
Scott Beatson PhD
NHMRC Howard Florey Research Fellow
School of Molecular and Microbial Sciences
University of Queensland
Brisbane QLD 4072
Australia
Tel: +61 7 33654863
Fax: +61 7 33654699
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