Represents the Pms1 algorithm developed by Rajasekaran et al.
Note: There are various known problems with the motif finding in SeqAn. We plan to fix this in an upcoming release.
The type of sequences to be analyzed.
The Rng specialization to use for random number generation.
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
|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)|
|Represents the main function which is used to start the search for noticeable motif patterns. (MotifFinder)|
|Gets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned. (MotifFinder)|
|Gets number of motifs in the MotifFinder. (MotifFinder)|
SeqAn - Sequence Analysis Library - www.seqan.de