[BioC] Extracting protein sequence associated to UCSC transcript id

[rcaloger]

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 at 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 at 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 at unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it