Function

em

Represents the EM algorithm as used by MEME.

Include Headers

seqan/find_motif.h

Parameters

A StringSet of frequency distributions. Types: StringSet | |

An iterator pointing to the first input sequence of a given dataset. Types: Iterator | |

The number of input sequences. | |

The size of the motif. | |

The oops_model object. Types: Oops | |

The zoops_model object. Types: Zoops | |

The tcm_model object. Types: Tcm | |

The probability of sequence having a motif occurence. | |

The probability of starting a motif occurence Remarks: |

Remarks

This version of EM is used in the MEME program of Bailey and Elkan. It is a Bayesian
variant of the basic EM which allows multiple occurrences of a motif in any sequence and can
therefore be performed on sequences of one of the model types Oops, Zoops and
Tcm. We use the EM algorithm of MEME for the refinement step of PROJECTION.

SeqAn - Sequence Analysis Library - www.seqan.de