[EMBOSS] ORF selection with EMBOSS

[Andres Pinzon]

D'accord ;)

Best

On Tue, Dec 6, 2011 at 9:20 AM, Hervé Ménager <hmenager at pasteur.fr> wrote:
> 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<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