| Class Specialization EPatternBranching Represents the ePatternBranching algorithm of Davila and Rajasekaran.
MotifFinder
EPatternBranching
MotifFinder<TValue, EPatternBranching> Parameters
TValue | The type of sequences to be analyzed. Types: AminoAcid, Dna
Specialization of MotifFinder Metafunctions
Value | Type of the items in the container. (MotifFinder)
Functions
displayResult | 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)
findMotif | Represents the main function which is used to start the search for noticeable motif patterns. (MotifFinder)
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. Example Programs Motif Finder SeqAn - Sequence Analysis Library - www.seqan.de