  We showed in this paper that similarity network can be used as an powerful
tools to study the relationship of tRNA genes. We constructed a network of 3719
tRNA gene sequences using simplest alignment and studied its topology, degree
distribution and clustering coefficient. It is found that the behavior of the
network shift from fluctuated distribution to scale-free distribution when the
similarity degree of the tRNA gene sequences increase. tRNA gene sequences with
the same anticodon identity are more self-organized than the tRNA gene
sequences with different anticodon identities and form local clusters in the
network. An interesting finding in our studied is some vertices of the local
cluster have a high connection with other local clusters, the probable reason
is given. Moreover, a network constructed by the same number of random tRNA
sequences is used to make comparisons. The relationships between properties of
the tRNA similarity network and the characters of tRNA evolutionary history are
discussed.
