Class Specialization
Represents the Pms1 algorithm developed by Rajasekaran et al.
MotifFinder<TValue, Pms1>
Include Headers
The type of sequences to be analyzed.
Types: AminoAcid, Dna
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
ValueType of the items in the container. (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 -

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