.. Structural Motifs documentation master file, created by sphinx-quickstart on Mon Jan 29 16:17:32 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. image:: img/StruM_logo.png :height: 300px ======================================================================== StruMs: Structural Motifs documentation ======================================================================== Structural Motifs provide a way to represent DNA motifs based on the shape of the DNA instead of the DNA sequence. These motifs may represent the preferences driving specificity of transcription factors for their binding sites. For more information about the underlying model of StruMs, refer to :doc:`intro`. The package described here provides a framework for computing and working with StruMs, based on DNA shape features from the `Dinucleotide Property DataBase `_. Currently available capabilities include: * Train models from known binding sites * Use expectation maximization to find *de novo* motifs * Provide utility to incorporate additional quantitative features, e.g. DNase hypersensitivity. * Score matches of the motif to novel sequences ------------------------------------------------------------------------ Contents ------------------------------------------------------------------------ .. toctree:: :maxdepth: 2 intro installation examples code ======================================================================== Indices and tables ======================================================================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`