[BioC] Extracting protein sequence associated to UCSC transcript id

rcaloger raffaele.calogero at gmail.com
Tue Jan 7 15:54:34 CET 2014

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 
Indeed the protein sequence is present in the UCSC genome browser, but I 
do not know how to grab it.
Any suggestion?


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
www:   http://www.bioinformatica.unito.it

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