Class Specialization

EPatternBranching

Represents the ePatternBranching algorithm of Davila and Rajasekaran.

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

EPatternBranching |

Include Headers

seqan/find_motif.h

Remarks

The EPatternBranching algorithm is an extended version of the
well-known PatternBranching algorithm which was developed by Price et al.
It is a heuristic algorithm such as Projection and uses a pattern-based
approach. The algorithm searches in the space of possible motifs. The basic concept
of EPatternBranching remains the same as in the original PatternBranching algorithm
Starting from each l-mer x in the input sequences the algorithm iteratively searches
around the vicinities of x and finds the best neighbors by applying a specific function
called bestNeighbors. At the end of each step, it selects those patterns from the set
of best neighbors that fulfill a particular condition and that are therefore qualified
for being a motif instance.

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