Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.

ABSTRACT: A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral alg

SUBMITTER: Saw AK 

PROVIDER: S-EPMC6403383 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature