An Affinity Propagation-Based DNA Motif Discovery Algorithm

Algorithm 1

APMotif.

Input:   =

Output: () motif instances set

()

() for each l-mer ∈ ,   do

()  Construct cluster

() for each   do

()  Use AP clustering and a filtering rule to generate cluster

() for each   do

()  Use EM algorithm to generate and

() Calculate ,

() for   to   do

()   for each l-mer y∈   do

()    Calculate

()    Add to

() Output