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prothint website  
ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

Environment Modules

Run module spider prothint to find out what environment modules are available for this application.

System Variables

  • HPC_PROTHINT_DIR - installation directory
  • HPC_PROTHINT_BIN - executable directory

Additional Information

Because the GeneMark-ES executable is not installed in our ProtHint environment, you will need to add the following argument to all of your commands in order to prevent ProtHint from trying to run it:

 --geneSeeds $HPC_PROTHINT_DIR/example/input/genemark.gtf


If you publish research that uses prothint you have to cite it as follows:

Please cite

- ProtHint:
- Spaln: