Metrics on the basis of optimal alignment of biomolecular sequences
Background: It is important for biomolecular sequences analysis to have an appropriate way for comparing them. From the point of view of advanced methods of data analysis, the most preferred way for comparing objects is a dissimilarity measure, possessing metric’s properties. From the other side,from the point of view of the molecularbiology,it is important to take into account biological features of the compared objects. Besides, the computational eﬀectiveness and the possibility of further using convenient instruments of data analysis are also important. There are a number of ways for comparing biomolecular sequences, though no one of them possess the all required properties. Methods: This paper proposes a simple enough way for computing metrics for biomolecular sequences. The proposed approach, following traditional ways for biomolecular sequences comparing, is based on ﬁnding an optimal pairwise alignment and on the model of mutual changes of amino acids at the process of evolution. Concluding Remarks: It is proved that the proposed dissimilarity measure is a metric. So, it can be used at the advanced methods of data analysis, saving computational advantages of support vector machine without introducing features of objects or(and) an inner product. The experimental results conﬁrm usability of the proposed metric for membrane glycoprotein classiﬁcation.