├── LICENSE ├── data ├── fasta │ ├── AimR-TPR_seed_from_Stokar-Avihail_et_al.fasta │ ├── AimR_seed_from_Erez_et_al.fasta │ ├── SHP_seed.fasta │ └── ref_receptors.faa ├── hmm_libraries │ ├── HTH.hmm │ ├── SHP.hmm │ └── TPRs.hmm └── metadata │ ├── interproscan_vs_ref_receptors.tsv │ ├── reference_systems_metadata.tsv │ └── tprpred_vs_ref_receptors.tsv ├── predisi ├── CITE ├── JSPP.class ├── JSPP.java ├── doc │ └── jspp │ │ ├── SearchMatrix.html │ │ └── SignalPeptidePredictor.html ├── jspp │ ├── SearchMatrix.class │ ├── SequenceLengthException.class │ └── SignalPeptidePredictor.class ├── matrices(SearchMatrix-objects) │ ├── eukarya.smx │ ├── gramn.smx │ └── gramp.smx └── readme.txt ├── readme.md ├── rrnpp_detector.py ├── rrnpp_detector ├── __init__.py ├── check_args.py ├── filter.py ├── integrate_annotations.py ├── launcher.py ├── make_summary.py ├── preprocessing.py ├── search_small_orfs.py └── wrappers.py ├── signalp-5.0b.tar.gz └── tprpred ├── AlignRep.pm ├── CITE ├── Erf.pm ├── README 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