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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support