Human polyomaviruses identification by logic mining techniques

The approach presented in this work is successful as it discovers several logic rules that effectively characterize the different five studied polyomaviruses. The individuated logic rules are able to separate precisely one viral type from the other and to assign an unknown DNA sequence to one of the five analyzed polyomaviruses.The data mining analysis is performed by considering the complete sequences of the viruses and the sequences of the different gene regions separately, obtaining in both cases extremely high correct recognition rates.Phylogenetic analysis is a technique used to perform species classification through DNA sequences analysis [1]. It examines sequence divergence or similarity through the alignment of DNA sequences. Recently, a new technique, named logic data mining, has been introduced and applied in species classification through DNA barcode, a short fragment of mitochondrial DNA composed of few hundreds of bases from which it is possible to extract the information needed to classify living species [2]. This technique allows finding patterns of nucleotides in the DNA barcode of a given species that characterizes it and allows distinguishing one species from the others. A pattern is defined as a set of positions of the DNA sequence whose corresponding nucleotides completely characterize the species. The logic data mining technique provides a sort of fingerprinting of the species and has been shown to allow a correct classification of new individuals. In this work we apply this technique to the classification of polyomaviruses. Human polyomaviruses are small double stranded DNA viruses of about 5 kb in length which belong to the Polyomaviridae family. Up to 2008, five human polyomaviruses have been identified and characterized: BK (BKPyV), JC (JCPyV), KI (KIPyV), WU (WUPyV) and MC (MCPyV) polyomaviruses. BKPyV and JCPyV were both uncovered in 1971. BKPyV was first identified in the urine of a kidney transplant patient [3], while JCPyV was uncovered