Hi Ekta,

You'll find complete data sets in our downloads section:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/

Let me know if you have any additional questions.

-
Greg Roe
UCSC Genome Bioinformatics Group

On 3/27/11 5:31 PM, Ekta Khurana wrote:
> Hi,
>
> I want to download CDS multiple sequence alignments for all Gencode
> transcripts.
> > From the download server I can download alignments for refseq and UCSC exons
> but not
> Gencode transcripts.
> I can do this for some transcripts from the Table Browser but the dataset is
> too huge to download all of it.
> Could someone please let me know if there is a way to download the entire
> set .
>
> Thanks in advance for the reply,
> Ekta
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