[EMBOSS] ORF selection with EMBOSS

[Hervé Ménager]

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