Clustering DNA sequences using the out-of-place measure with reduced n-grams.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Theoretical Biology

• Publication date

  2016-10-07

• Fields of study

  Biology, Mathematics, Computer Science, Medicine

• Identifiers
  DOI 10.1016/j.jtbi.2016.06.029PMID 27375217
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An improved model for whole genome phylogenetic analysis by Fourier transform.

  2015cited by this paper
• CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

  2015cited by this paper
• New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

  2014cited by this paper
• K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.

  2014cited by this paper
• Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

  2014cited by this paper
• Global comparison of multiple-segmented viruses in 12-dimensional genome space.

  2014cited by this paper
• Genomic taxonomy boost by lexical clustering

  2014cited by this paper
• Alignment free comparison: k word voting model and its applications.

  2013cited by this paper
• MetaID: A novel method for identification and quantification of metagenomic samples

  2013cited by this paper
• The textcat Package for n-Gram Based Text Categorization in R

  2013cited by this paper
• Real Time Classification of Viruses in 12 Dimensions

  2013cited by this paper
• runmlwin : A Program to Run the MLwiN Multilevel Modeling Software from within Stata

  2013cited by this paper
• Suite of Tools for Statistical n-Gram Language Modeling for Pattern Mining in whole genome Sequences

  2012cited by this paper
• Alignment-free phylogeny of whole genomes using underlying subwords

  2012cited by this paper
• Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)

  2012cited by this paper
• Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

  2012cited by this paper
• Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders.

  2011cited by this paper
• A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications

  2011cited by this paper
• N-gram analysis of 970 microbial organisms reveals presence of biological language models

  2011cited by this paper
• Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations.

  2010cited by this paper
• A Novel Construction of Genome Space with Biological Geometry

  2010cited by this paper
• Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

  2009cited by this paper
• Genomic DNA k-mer spectra: models and modalities

  2009cited by this paper
• Estimation of bacterial species phylogeny through oligonucleotide frequency distances.

  2009cited by this paper
• Scientific Computation: Phylogenetic tree construction

  2009cited by this paper
• Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

  2009cited by this paper
• Bird evolution: testing the Metaves clade with six new mitochondrial genomes

  2008cited by this paper
• Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

  2008cited by this paper
• A statistical method for alignment-free comparison of regulatory sequences

  2007cited by this paper
• Sorting Stably, in Place, with O(n log n) Comparisons and O(n) Moves

  2007cited by this paper
• n-Gram-based classification and unsupervised hierarchical clustering of genome sequences

  2006cited by this paper
• Genomic Classification Using an Information-Based Similarity Index: Application to the SARS Coronavirus

  2005cited by this paper
• Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences

  2005cited by this paper
• New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i).

  2004cited by this paper
• Alignment-free sequence comparison-a review

  2003cited by this paper
• Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.

  2002cited by this paper
• An information-based sequence distance and its application to whole mitochondrial genome phylogeny

  2001cited by this paper
• Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris.

  2000cited by this paper
• Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences

  1996cited by this paper
• N-gram-based text categorization

  1994cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• A measure of the similarity of sets of sequences not requiring sequence alignment.

  1986cited by this paper
• Fast Pattern Matching in Strings

  1977cited by this paper
• IEEE / ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 1 Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison

  year unknowncited by this paper

• Clustering methods for Categorical Time Series and Sequences : A scoping review

  2025cites this paper
• Using transfer learning models for DNA sequence similarity via fCGR method

  2025cites this paper
• Efficient TF-IDF method for alignment-free DNA sequence similarity analysis.

  2025cites this paper
• A Bibliometric Analysis

  2022cites this paper
• On the Verge of Life: Distribution of Nucleotide Sequences in Viral RNAs

  2020cites this paper
• A study and identi�cation of COVID-19 viruses using N-grams with Naïve Bayes, K-Nearest Neighbors, Arti�cial Neural Networks, Decision tree and Support Vector Machine

  2020cites this paper
• A novel alignment-free DNA sequence similarity analysis approach based on top-k n-gram match-up.

  2020cites this paper
• A study and identification of COVID-19 viruses using N-grams with Naïve Bayes, K-Nearest Neighbors, Artificial Neural Networks, Decision tree and Support Vector Machine

  2020cites this paper
• A geometric characterization of DNA sequence

  2019cites this paper
• Phylogenetic analysis of protein sequences based on a novel k-mer natural vector method.

  2019cites this paper
• Discrete Wavelet Packet Transform Based Discriminant Analysis for Whole Genome Sequences

  2019cites this paper
• 2D GRAPHICAL REPRESENTATION OF DNA SEQUENCE BASED ON HORIZON LINES FROM A PROBABILISTIC VIEW REPRESENTAÇÃO GRÁFICA 2D DA SEQÜÊNCIA DE DNA BASEADA EM LINHAS

  2018cites this paper
• Discriminant Analysis and Normalization Methods for Next-Generation Sequencing Data

  2018cites this paper
• A Novel Real-Time Genome Comparison Method Using Discrete Wavelet Transform

  2017cites this paper
• Compressive sampling for phenotype classification

  2017cites this paper
• Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

  2017cites this paper
• Strategies for Identifying the Optimal Length of K-mer in a Viral Phylogenomic Analysis using Genomic Alignment-free Method

  2016cites this paper