├── Dockerfile ├── README.md ├── __pycache__ └── utils.cpython-36.pyc ├── docs ├── SPOTRNA2_pipeline.png └── benchmark_results.png ├── nt_database └── empty_db.fasta ├── requirements.txt ├── run_spotrna2.sh ├── sample_run ├── 6ufj.fasta ├── sample_seq.fasta ├── sample_seq_features │ ├── sample_seq.a2m │ ├── sample_seq.aln │ ├── sample_seq.bla │ ├── sample_seq.bpseq │ ├── sample_seq.bpseq.unknotted │ ├── sample_seq.cm │ ├── sample_seq.ct │ ├── sample_seq.db │ ├── sample_seq.dbn │ ├── sample_seq.dca │ ├── sample_seq.fasta │ ├── sample_seq.log_gremlin │ ├── sample_seq.msa │ ├── sample_seq.out │ ├── sample_seq.prob │ ├── sample_seq.pssm │ ├── sample_seq.sto │ ├── sample_seq.tfrecords │ ├── temp.a2m │ ├── temp.sto │ └── temp.txt └── sample_seq_outputs │ ├── sample_seq.bpseq │ ├── sample_seq.ct │ ├── sample_seq.prob │ └── sample_seq.st └── utils ├── FreeKnot ├── BpseqParser.pm ├── BpseqWriter.pm ├── BracketPairs.pm ├── COPYRIGHT ├── COPYRIGHT.txt ├── ChordModel.pm ├── CircleGraph.pm ├── DPParser.pm ├── DPWriter.pm ├── LICENSE ├── LICENSE.txt ├── MIS.pm ├── MWIS.pm ├── PrimitivePseudoknotExtractor.pm ├── README ├── README.txt ├── ScoringFunctions.pm ├── VertexSubset.pm └── remove_pseudoknot.pl ├── SPOT-RNA2.py ├── __pycache__ └── utils.cpython-36.pyc ├── bpRNA.pl ├── bpseq2dbn.py ├── getpssm.pl ├── parse_blastn_local.pl ├── reformat.pl ├── seqkit └── utils.py /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jaswindersingh2/SPOT-RNA2/HEAD/Dockerfile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jaswindersingh2/SPOT-RNA2/HEAD/README.md -------------------------------------------------------------------------------- /__pycache__/utils.cpython-36.pyc: -------------------------------------------------------------------------------- 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