PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets

Algorithm 1

PairMotifChIP.

Input: , optional parameters and

Output: a set of motifs

(1) , set the threshold of extracting pairs of -mers

(2) for each pair of -mers () in   do

(3)  if   then

(4)    add to

(5) for each pair of -mers  do

(6)  if   then

(7)     add to

(8)  if   then

(9)     add to

(10) cluster the -mers in

(11)  for each obtained cluster do

(12)  align substrings in it and fetch a segment with high information content to form a motif

(13)  add to

(14) return