Class Specialization
Projection
Represents the PROJECTION algorithm of Buhler and Tompa.
MotifFinder
Projection
MotifFinder<TValue, Projection>
Parameters
TValue
The type of sequences to be analyzed.
Types: AminoAcid, Dna
Specialization of
Metafunctions
ValueType of the items in the container. (MotifFinder)
Functions
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)
Remarks
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).
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de