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

Year 2019, Volume: 7 Issue: 4, 405 - 416, 30.10.2019

Berat Dogan

https://doi.org/10.17694/bajece.540873

Abstract

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 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.0000-0003-4810-1970

Keywords

ClustalW, ND5 proteins, Phylogenetic analysis, Protein sequence similarity

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