Hello John, To use all BLAST+ functions with Galaxy, a local or cloud instance is needed. The public main Galaxy instance does not host tblastn, only megablast (based on blastn) - and only for certain databases. Many biologists prefer using a cloudman instance as much of the set-up is already packaged and it does not require an investment in local hardware/servers/data & tool setup. Details can be found in our wiki at: Cloudman: http://usegalaxy.org/cloud Local instance: http://getgalaxy.org The best mailing list for local or cloud instance support, should you run into issues (or just want to follow the technical threads), is galaxy-dev@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Hopefully this helps! Jen Galaxy team On 10/3/12 7:54 AM, John DeFilippo wrote:

We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D

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