ArticleScientific reports2019
Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- Clustering methods for categorical time series and sequences : a scoping review.BMC medical research methodology · 2026Article
- Motif distribution in genomes gives insights into gene clustering and co-regulation.Nucleic acids research · 2025Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification.PloS one · 2024Article
- 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity ofLife (Basel, Switzerland) · 2022Article
- Virus genomics: what is being overlooked?Current opinion in virology · 2022Review
- Can wood-decaying urban macrofungi be identified by using fuzzy interference system? An example in Central European Ganoderma species.Scientific reports · 2021Article
- Significant non-existence of sequences in genomes and proteomes.Nucleic acids research · 2021Article
- Non-standard bioinformatics characterization of SARS-CoV-2.Computers in biology and medicine · 2021Article
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Whole-GenomeGenes · 2020Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
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 algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.
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