Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

Algorithm 1

Simple-Align algorithm.

Input: Graph (, ), Graph (, ) such that

Output: Local alignment

()   Define as an array of sets with length

()    = Set of all local alignments of size one

()   for   to   do

()    for   to   do

()     

()     for   to   do

()      for   to   do

()          = ’th element of

()          = ’th element of

()     

()    end for

()   end for

()  end for

() end for

() return The LA with highest score among all LAs in