ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2010
A novel construction of genome space with biological geometry.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- A latent genetic subtype of major depression identified by whole-exome genotyping data in a Mexican-American cohort.Translational psychiatry · 2017Trial
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- Visualization Methods for DNA Sequences: A Review and Prospects.Biomolecules · 2024Review
- Exploring geometry of genome space via Grassmann manifolds.Innovation (Cambridge (Mass.)) · 2024Article
- A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets.Genomics · 2020Article
- A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance.Frontiers in genetics · 2019Article
- Large-Scale Genome Comparison Based on Cumulative Fourier Power and Phase Spectra: Central Moment and Covariance Vector.Computational and structural biotechnology journal · 2019Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- A novel fast vector method for genetic sequence comparison.Scientific reports · 2017Article
- A novel strategy for clustering major depression individuals using whole-genome sequencing variant data.Scientific reports · 2017Article
- Article
- Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.Genomics, proteomics & bioinformatics · 2016Article
- A new method to cluster DNA sequences using Fourier power spectrum.Journal of theoretical biology · 2015Article
- Mapping the space of genomic signatures.PloS one · 2015Article
- K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.Gene · 2014Article
- Effective gene prediction by high resolution frequency estimator based on least-norm solution technique.EURASIP journal on bioinformatics & systems biology · 2014Article
- Article
- AGP: a multimethods web server for alignment-free genome phylogeny.Molecular biology and evolution · 2013Article
- Real time classification of viruses in 12 dimensions.PloS one · 2013Article
- An integrative method for identifying the over-annotated protein-coding genes in microbial genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
Corrections and comments
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5 authors.
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Abstract
A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in R(N). It allows us to show that the SARS-CoV is most closely related to a coronavirus from the palm civet not from a bird as initially suspected, and the newly discovered human coronavirus HCoV-HKU1 is more closely related to SARS than to any other known member of group 2 coronavirus. Furthermore, we reconstructed the phylogenetic tree for 34 lentiviruses (including human immunodeficiency virus) based on their whole genome sequences. Our genome space will provide a new powerful tool for analyzing the classification of genomes and their phylogenetic relationships.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.