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