Sequence comparison in the form of alignment plays a crucial role in the area of bioinformatics. However,
alignment is commonly restricted by the number of aligned sequences. To address this problem, we presented a 2D
pattern matching algorithm for comparing protein sequences. The new algorithm which is an alignment-free comparison
is capable of allowing fast comparison even among a large number of protein sequences. The simulation on the artificial
sequences indicated that our method would be robust. And the experiment on real protein sequences showed that our
method would be effective.
Keywords: Alignment, alignment-free comparison, binary tree, graphical representation, phylogenetic tree, sequence,
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