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Welcome to the ssHMM documentation! Background Scope License
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Welcome to the ssHMM documentation!

ssHMM stands for "Sequence-Structure Hidden Markov Model". It is an RNA motif finder and recovers sequence-structure motifs from RNA-binding protein data.

Background

RNA-binding proteins (RBPs) play a vital role in the post-transcriptional control of RNAs. They are known to recognize RNA molecules by their nucleotide sequence as well as their three-dimensional structure. ssHMM combines a hidden Markov model (HMM) with Gibbs sampling to learn the joint sequence and structure binding preferences of RBPs from high-throughput RNA-binding experiments, such as CLIP-Seq. The model can be visualized as an intuitive graph illustrating the interplay between RNA sequence and structure.

Scope

ssHMM was developed for the analysis of data from RNA-binding assays. Its aim is to help biologists to derive a binding motif for one or a number of RNA-binding proteins. ssHMM was written in Python and is a pure command-line tool.

License

The project is licensed under the GNU General Public License.

.. toctree::
    :maxdepth: 2
    :caption: Contents:

    Installation/index
    tutorial
    Output/index
    preprocess
    Reference/index
    GitHub <https://github.molgen.mpg.de/heller/ssHMM>