[EMBOSS] ORF selection with EMBOSS

[Andres Pinzon]

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 <jison at 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
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>
>>>
>>>
>>
>
>
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-- 
Andrés Pinzón