An alignment-free method for bulk comparison of protein sequences from different species

The available number of protein sequences rapidly increased with the development of new sequencing techniques. This in turn led to an urgent need for the development of new computational methods utilizing these data for the solution of different biological problems. One of these problems is the comparison of protein sequences from different species to reveal their evolutional relationship. Recently, several alignment-free methods have been proposed for this purpose. Here in this study, we also proposed an alignment-free method for the same purpose. Different from the existing methods, the proposed method not only allows for a pairwise comparison of two protein sequences, but also it allows for a bulk comparison of multiple protein sequences simultaneously. Computational results performed on gold-standard datasets showed that, bulk comparison of multiple sequences is much faster than its pairwise counterpart and the proposed method achieves a performance which is quite competitive with the state-of-the-art alignment-based method, ClustalW.

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