Hello,

The general analysis path would be:

1 - Map the transcripts to a reference genome to obtain location
    coordinates.
    One option is BLAST, which has a wrapper in the Tool Shed
    See http://galaxyproject.org/wiki/Tool%20Shed

2 - Import known protein-coding and non-protein coding tracks.
    See "Get Data"

3 - Use an intersection query to identify overlapping regions between
    the datasets to obtain annotation
    See "Operate on Genomic Intervals"

The first mapping step would require a local or cloud instance, the other steps can be done within the public Galaxy or your own.
Help: http://galaxyproject.org/wiki/Admin/Get%20Galaxy

Best wishes for your project!

Jen
Galaxy team

On 9/29/11 9:35 AM, dongdong zhaoweiming wrote:
Hi, I want to evaluate wherther my assembly transcripts produced by
trinity is protein-coding or notcoding. I found two methods which are
"txCdsPredict" program from the UCSC(John R Prensner,2011) and Codon
Substitution Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy
can do this? Thanks a lot!
weimin zhao



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___________________________________________________________
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