ArticleBMC bioinformatics2008
Barcodes for genomes and applications.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed.
- Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.mSystems · 2025Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.BMC bioinformatics · 2024Article
- Article
- MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes.PloS one · 2023Article
- Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.Nature communications · 2022Article
- Bibliometric analysis of tuberculosis molecular epidemiology based on CiteSpace.Frontiers in public health · 2022Article
- Article
- A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.Briefings in bioinformatics · 2021Article
- PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing.Bioinformatics (Oxford, England) · 2020Article
- Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach.PloS one · 2020Article
- The statistical power ofSynthetic and systems biotechnology · 2019Article
- A microbial factory for defensive kahalalides in a tripartite marine symbiosis.Science (New York, N.Y.) · 2019Article
- Article
- PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.Nucleic acids research · 2018Article
- Article
- Article
- Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.BMC bioinformatics · 2016Article
- Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.BioMed research international · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEach genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.
resultsWe found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness.
conclusionThese and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.