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
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:
Hi Jack, Scott,
This does look to be the best solution at the moment and appears that may
have been a quick solution here in the past.
I will look at implementing this for the next release. This may take the
form of an extra check box on the ³minimum open reading frame² window, so
that Artemis kn
Hi,
If it's only a quick and early screening without any gene prediction
Blastxtract (found in pubmed), can manage, search and graphically
visualise pre-computed blastx/fastx results of genomic sequence, once
installed.
Marcus
On Mon, 2007-06-25 at 17:03 +0200, Jack van de Vossenberg wrote:
> D
Jack,
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, especiall
Good point Torston, this is the way I do it too, apologies for
forgetting to mention the start codons in my earlier post! I tend to
use more N's at either end too, so it is really obvious by eye when
looking at a "fake" translated ORF in later analyses.
It is a great idea to re-order your c
