To use BLASTX directly, a wrapper is available in the Tool Shed for
with a local or cloud instance of Galaxy. Please see:
Another option is to map against the target genome, then compare
coordinates of those hits with the coordinates of known annotation
represents CCDS or alternate protein tracks of interest. UCSC,
and other sources under "Get Data" can be used to import BED/Interval
data directly into Galaxy. Compare coordinates using tools in the
"Operate on Genomic Intervals". There are other tools that compare
coordinates (Bed Tools, etc.) but these are a good place to start.
A several of our tutorials have examples of how to compare
including "Galaxy 101" and protocols 1 & 4 of "Using Galaxy". The
themselves also have help directly on the tool forms.
If you used an Ensembl annotation track, then tools in the group
Diversity -> KEGG and GO" might be of interest to you. The UCSC "Known
Genes" track also has some extra tables (http://genome.ucsc.edu
you may find interesting to pull in and consider, if you decided to
that as the annotation track to compare against. Most (if not all) of
this data can linked together either through coordinates or
but it is not available for all genomes, you will have to check at the
For predictive domain analysis using conserved genomic data, the tools
in "Fetch Alignments" function with MAF inputs. A bed file of hits can
be used to query out data from multiple species, obtain sequence, etc.
for downstream analysis. Protocol 5 in the "Using Galaxy" paper above
has a walk-through of how this can be done. If the public Main server
does not have the MAF data for your genome, and it is small, it is
possible to use one from the history. If it is larger, using a local
cloud Galaxy would be recommended.
Be sure to check the Tool Shed if there is a specific tool that you
looking for. If it is not there now, you could ask if someone has it
if it is the process of being wrapped (on the development list:
email@example.com). And keep checking back, more tools are added
Galaxy Support and Training