Alignment-free similarity analysis for protein sequences based on fuzzy integral

Abstract

Sequence comparison is an essential part of modern molecular biology research. In this study, we estimated the parameters of Markov chain by considering the frequencies of occurrence of the all possible amino acid pairs from each alignment-free protein sequence. These estimated Markov chain parameters were used to calculate similarity between two protein sequences based on a fuzzy integral algorithm. For validation, our result was compared with both alignment-based (ClustalW) and alignment-free methods on six benchmark datasets. The results indicate that our developed algorithm has a better clustering performance for protein sequence comparison.

A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets

“…We use MEGA7 to construct a phylogenetic tree for each dataset. Our constructed phylogenetic trees are then compared with the results obtained from some other advanced genome sequence comparison methods like Feature Frequency Profiles (FFP) method [ 30 ], Fuzzy Integral Similarity method [ 34 ], ClustalW method, Multiple Encoding Vector method [ 40 ], Fast Vector method [ 40 ], Weighted Measure method [ 42 ], Probabilistic method [ 23 ], K-mer method [ 29 ]. From the results, we can see the efficiency in terms of time complexity and accuracy of our new method is better than or equal to all other previously published methods on the same datasets.…”

“…4 ), with phylogenetic trees (Supplementary Figs. S1, S2, S3, and S4) constructed by other methods [ 30 , 34 , 40 ] shown in the supplementary file. According to the Feature frequency profiles (FFP) [ 30 ] method using k = 7 shown in Fig.…”

“…Overall in FFP methods, all eight types of species are not classified properly. The phylogenetic tree constructed according to the Fuzzy integral similarity method [ 34 ] is shown in Supplementary Fig. S2.…”

“…Now we compare our phylogenetic tree with those given in Figs. S5, S6, S7, and S8 (in the supplementary file) obtained by other methods [ 30 , 34 , 40 ]. Phylogenetic tree generated by the Fuzzy integral similarity method [ 34 ] as given in Fig.…”

“…ICCV method is found to be more robust and efficient. Now we mention the fuzzy integral similarity method [ 34 ], which is also under the classification of k-mer or word frequency method. In this method, the Markov chain is used as an estimated parameter to calculate similarity scores between two DNA sequences.…”