On Thu, 5 Jul 2007, Richard Holland wrote:
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So the question is: if I ask for 5'UTR+upstream-800, shouldn't I
always be getting at least 800 bp of upstream sequence, irrespective
of the absence/presence of the 5'UTR?
The upstream/downstream generator adds extra bases relative to the
start/end of the feature selected (5'UTR, 3'UTR, gene flank, etc.). If
that feature does not exist, then there is no coordinate to start taking
extra bases from, and so you can't get additional sequence.
Hi Guys,
I can see both points of view and I think there is nothing in our software
to stop us just returning 800bp of upstream flank sequence for the genes
without a UTR. I am just not sure what the best policy is - is it more
confusing when you ask for 800bp upstream + UTR for all genes to get a "no
UTR response" for the ones without a UTR or just silently get the
800bp. I think as usual the best solution will be some sort of middleground where
the output is 800bp but with a clear indication of "no UTR". We are going
to review all our sequence outputs soon with maybe some clearer markup of
coding vs non-coding etc so this may become part of that solution.
If anyone has any suggestions please forward them to us.
Best wishes
Damian
cheers,
Richard
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