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#413 checktrans to report longest ORF
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?
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.
>