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The naive approach

Let us define a directed graph G`=(V`,E`), where $V\lq =\{\mbox{existing $k$ -mers}\}$and an edge E`=(v1,v2) exists iff the last k-1 characters of v1 match the first k-1 characters of v2 (i.e., it is possible that v2's index in T, is the successor of v1's index.

The problem is now to find a Hamiltonian path in the directed graph G. However, it is a common knowledge that the Hamilonian path problem is NP-Complete. Therefore, this solution cannot be used for large input sets.



Peer Itsik
2001-02-01