Class Specialization
Represents the PROJECTION algorithm of Buhler and Tompa.
Note: There are various known problems with the motif finding in SeqAn. We plan to fix this in an upcoming release.
MotifFinder<TValue, Projection, TRng>
Include Headers
The type of sequences to be analyzed.
Types: AminoAcid, Dna
The Rng specialization to use for random number generation.
Default: GetDefaultRng<MotifFinderClass>::Type
The Projection algorithm is a heuristic algorithm that does not guarantee that the unknown motif will be found every time. We can increase the chance of success by performing a large number of independent trials to generate multiple guesses. In each trial, Projection makes a preselection of sets of length-l patterns called l-mers which are likely to be a collection of motif instances (filtering step) and refines them by some local searching techniques, e.g. EM algorithm, Gibbs Sampling etc (refinement step).
Specialization of
ValueType of the items in the container or behind an iterator. (MotifFinder)
displayResultDisplays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate. (MotifFinder)
findMotifRepresents the main function which is used to start the search for noticeable motif patterns. (MotifFinder)
getMotifGets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned. (MotifFinder)
motifCountGets number of motifs in the MotifFinder. (MotifFinder)
Example Programs
SeqAn - Sequence Analysis Library -

Page built @2013/07/11 09:12:39