[Genome] CCDS protein sequences

[Ann Zweig]

Hello Jittima,

     Because we generate the protein sequence on the fly, it is not 
trivial to get the protein sequence for only part of a CCDS gene.  This 
is because, given only a part of the gene, it is not possible for us to 
tell which frame to start generating the protein from.

     It is possible, however, to get the protein for the entire CCDS 
gene. You can do this from the gene details page: click on the CCDS gene 
in question, then click on the 'protein' hyperlink.  From there you can 
calculate your position and extract the protein part you are interested in.

    Alternatively you can use the exonStarts and exonFrames fields in 
the ccdsGene table to figure out the frame.  Then you could translate 
the genomic sequence yourself.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


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Jittima Piriyapongsa wrote:
> Hi,
> 
> I have a question regarding CCDS protein sequence. I have a list of 
> genomic coordinates corresponding to a part or whole exon of CCDS 
> gene. Is there any way to get the part of protein sequences 
> corresponding to those regions?
> 
> Thank you.
> Jittima
> 
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