In theory, you should be able to get the cds regions using e.g. the
Homo.sapiens package, but it seems kind of tough to retrieve those for UCSC
Known Gene identifiers (assuming that is what you have). Marc Carlson could
probably help more.

Michael





On Wed, Jan 8, 2014 at 6:31 AM, rcaloger <raffaele.calogero@unito.it> wrote:

> Dear Michael,
> thank for the kind suggestion but unfortunately it does not solve my
> problem because, using the approach you are suggesting, I do not have
> access to the position of the start codon for the different isoforms.
> Cheers
> Raf
>
>
> On 07/01/14 16:44, Michael Lawrence wrote:
>
>> If you had the transcript coordinates (as GRangesList, perhaps from an
>> exonsBy() on a TranscriptDb) you could use extractTranscriptsFromGenome()
>> and translate, see the GenomicFeatures vignette for an example.
>>
>> Michael
>>
>>
>> On Tue, Jan 7, 2014 at 6:54 AM, rcaloger <raffaele.calogero@gmail.com>
>> wrote:
>>
>>  Hi,
>>> In order to validate fusion products I need to be sure that the peptides
>>> encoded by the the two fused proteins are in the same frame.
>>> I have now a function that allows to confirm the protein1 and protein2
>>> have sequences located in the same frame.
>>> However, I got stack to retrieve those proteins sequences from UCSC. I
>>> did
>>> not found a quick way to retrieve the protein sequence associated to a
>>> UCSC
>>> ID.
>>> Indeed the protein sequence is present in the UCSC genome browser, but I
>>> do not know how to grab it.
>>> Any suggestion?
>>> Cheers
>>> Raffaele
>>>
>>> --
>>>
>>> ----------------------------------------
>>> Prof. Raffaele A. Calogero
>>> Bioinformatics and Genomics Unit
>>> MBC Centro di Biotecnologie Molecolari
>>> Via Nizza 52, Torino 10126
>>> tel.   ++39 0116706457
>>> Fax    ++39 0112366457
>>> Mobile ++39 3333827080
>>> email: raffaele.calogero@unito.it
>>>         raffaele[dot]calogero[at]gmail[dot]com
>>> www:   http://www.bioinformatica.unito.it
>>>
>>> _______________________________________________
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>>>
>>>
>
> --
>
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> MBC Centro di Biotecnologie Molecolari
> Via Nizza 52, Torino 10126
> tel.   ++39 0116706457
> Fax    ++39 0112366457
> Mobile ++39 3333827080
> email: raffaele.calogero@unito.it
>        raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
>
>

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