Class Specialization

Pms1

Represents the Pms1 algorithm developed by Rajasekaran et al.

Note: There are various known problems with the motif finding in SeqAn. We plan to fix this in an upcoming release.

Pms1 |

Include Headers

seqan/find_motif.h

Parameters

The type of sequences to be analyzed. | |

The Rng specialization to use for random number generation. Default: |

Remarks

The exact Pms1 algorithm (Planted Motif Search 1) searches in the space
of possible motifs such as EPatternBranching. The procedure of the algorithm
is quite simple. For every l-mer in each input sequence the algorithm generates
all possible length-l patterns in the Hamming distance d -neighborhood of x .
The neighbor sets for each sequence are then intersected so that at the end of the process
we get a group of l-mers or a single l-mer that occur(s) in each input sequence with d
substitutions.

Specialization of

Metafunctions

Type of the items in the container or behind an iterator. (MotifFinder) |

Functions

Displays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate. (MotifFinder) | |

Represents the main function which is used to start the search for noticeable motif patterns. (MotifFinder) | |

Gets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned. (MotifFinder) | |

Gets number of motifs in the MotifFinder. (MotifFinder) |

Example Programs

SeqAn - Sequence Analysis Library - www.seqan.de