Class Specialization
PMS1
Represents the PMS1 algorithm developed by Rajasekaran et al.
PMS1 |
Specialization of
Metafunctions
Type of the items in the container. (MotifFinder) |
Functions
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) |
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