ProtHint
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Description
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 prothint.py commands in order to prevent ProtHint from trying to run it:
--geneSeeds $HPC_PROTHINT_DIR/example/input/genemark.gtf
Citation
If you publish research that uses prothint you have to cite it as follows:
Please cite
- ProtHint: https://doi.org/10.1093/nargab/lqaa026 - DIAMOND: https://doi.org/10.1038/nmeth.3176 - Spaln: https://doi.org/10.1093/bioinformatics/btn460