├── .gitignore ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _themes │ └── sphinx_rtd_theme │ │ ├── __init__.py │ │ ├── breadcrumbs.html │ │ ├── footer.html │ │ ├── layout.html │ │ ├── search.html │ │ ├── searchbox.html │ │ ├── static │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ └── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── theme.conf │ │ └── versions.html ├── make.bat └── source │ ├── .ipynb_checkpoints │ ├── Gappy_Kernel_IGF_Example-checkpoint.ipynb │ ├── mismatch_tutorial-checkpoint.ipynb │ ├── motifkernel-checkpoint.ipynb │ └── motiftutorial-checkpoint.ipynb │ ├── Gappy_Kernel.pdf │ ├── Gappy_Kernel_IGF_Example.ipynb │ ├── conf.py │ ├── examples.rst │ ├── gappy.rst │ ├── home.rst │ ├── index.rst │ ├── kernels.rst │ ├── mismatch.rst │ ├── mismatch_tutorial.ipynb │ ├── motif.rst │ ├── motiftutorial.ipynb │ └── notebook_data │ ├── fibroblast.fa │ ├── mafk.png │ ├── negative_IGF2BP123.fasta │ ├── oct4.png │ ├── positive_IGF2BP123.fasta │ └── stemcells.fa ├── requirements.txt ├── setup.py ├── strkernel ├── Tutorialdata │ ├── Gappy_Kernel_IGF_Example.ipynb │ ├── gappy_test.py │ ├── mismatch_test.py │ ├── motif_test.R │ ├── negative_IGF2BP123.fasta │ ├── negative_PUM2.fasta │ ├── positive_IGF2BP123.fasta │ └── positive_PUM2.fasta ├── __init__.py ├── gappy_kernel.py ├── gappy_trie.py ├── lib │ ├── __init__.py │ ├── mismatchTrie.py │ ├── motif.py │ └── motiftrie.py ├── mismatch_kernel.py └── motifkernel.py └── tests ├── __init__.py ├── test_gappy_kernel.py ├── test_gappy_trie.py ├── test_mismatch_kernel.py └── test_motif_kernel.py /.gitignore: -------------------------------------------------------------------------------- 1 | # python files 2 | __pycache__ 3 | *.pyc 4 | 5 | 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