| Class Specialization PMS1 Represents the PMS1 algorithm developed by Rajasekaran et al.
MotifFinder
PMS1
MotifFinder<TValue, PMS1> 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 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. Example Programs Motif Finder SeqAn - Sequence Analysis Library - www.seqan.de