Natural similarity measures between position frequency matrices with an application to clustering

@article{Pape2008NaturalSM,
  title={Natural similarity measures between position frequency matrices with an application to clustering},
  author={Utz J. Pape and Sven Rahmann and Martin Vingron},
  journal={Bioinformatics},
  year={2008},
  volume={24 3},
  pages={350-7}
}
MOTIVATION Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied problem in computational biology. The binding sites for one TF are represented by a position frequency matrix (PFM). The discovery of new PFMs requires the comparison to known PFMs to avoid redundancies. In general, two PFMs are similar if they occur at overlapping positions under a null model. Still, most… CONTINUE READING

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