Application Pipeline - drivenbyentropy/aptasuite GitHub Wiki

Given a valid configuration file, a typical pipeline might consist in importing the sequence information into AptaSUITE, and perform a motif search. Finally, this information is exported to file. For this, it is required to import the sequences from file, run structure prediction on all unique species and finally call AptaTRACE. This is archived as follows

java -jar aptasuite.jar -parse -predict -trace -config /path/to/configuration/file 

If, after completing the above call, the species are additionally to be clustered by sequence similarity, AptaCLUSTER can be called. Note that -parse and -predict do not have to be called again as this information will be loaded from disk.

java -jar aptasuite.jar -cluster -export clusters -config /path/to/configuration/file