Hi Andres,
From my point of view, it would do the job if I didn't have a _list_ of
genes as an input: I hence need to input a list of genes and get as an
output a list of the longest ORF computed for each gene. If I do this
directly with getorf and sizeseq, my understanding is that sizeseq won't
allow me to select the longest ORF for each input sequence. I can make
the loop myself, but I won't unless it is not ẗhere somewhere in EMBOSS ;).
Cheers,
Hervé
On 12/06/2011 01:53 PM, Andres Pinzon wrote:
Herve,
Have you tried using "getorf" and then "sizeseq"?
I think it will work. Then you could get the first sequence from the output.
Best,
On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<ji...@ebi.ac.uk> wrote:
A note of it is already on the SourceForge "Feature Requests" ...
J:)
Hi Jon,
That's exactly what would make me happy. Assuming it makes it easier for
you if I formulate officially this request, where do I need to send the
request?
Hervé
On 12/06/2011 12:00 PM, Jon Ison wrote:
Hi Hervé
Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to
report the
longest
ORF then that should be an easy enough option to add.
Cheers
Jon
Hi,
I have been using transeq and checktrans to find ORFs in DNA sequences.
I have an question regarding the selection of the ORFs in case
checktrans finds multiple ones in the result of transeq: I would like to
select the longest one automatically (assuming it is the correct one).
Is there any existing tool in EMBOSS (or alternatively in any Bio*
library) that does this job?
Cheers,
Hervé
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