ArticleFrontiers in bioengineering and biotechnology2020
KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.
Article in Frontiers in bioengineering and biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- Alignment-freeJournal of clinical microbiology · 2026Article
- A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification.BioData mining · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- Viral Sentry AI-Automated zoonotic surveillance and drug repurposing agent.Biology methods & protocols · 2026Article
- Elucidating Transitions ofJournal of computational biology : a journal of computational molecular cell biology · 2026Article
- Multidimensional Gene Space as an Approach for Analyzing the Organization of Genomes.International journal of molecular sciences · 2025Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.bioRxiv : the preprint server for biology · 2025Article
- Rapid, reference-free identification of bacterial pathogen transmission using optimized splitMicrobial genomics · 2025Article
- Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.PloS one · 2025Article
- DeepEnhancerPPO: An Interpretable Deep Learning Approach for Enhancer Classification.International journal of molecular sciences · 2024Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- Article
- CAIM: coverage-based analysis for identification of microbiome.Briefings in bioinformatics · 2024Article
- Article
- CAIM: Coverage-based Analysis for Identification of Microbiome.bioRxiv : the preprint server for biology · 2024Article
- Fast and Accurate Identification ofJournal of fungi (Basel, Switzerland) · 2023Article
- Synonymous nucleotide changes drive papillomavirus evolution.Tumour virus research · 2022Review
- K-mer based prediction ofMicrobial genomics · 2022Article
- An Alignment-Independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage.Biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Genomic DNA is the best "unique identifier" for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification. Although this approach is not novel, selecting the appropriate k-mer length to obtain the optimal resolution is rather arbitrary. However, it is a very important parameter for achieving the appropriate resolution for genome/sequence distances to infer biologically meaningful phylogenetic relationships. Thus, there is a need for a systematic approach to identify the appropriate k-mer from whole-genome sequences. We present K-mer-length Iterative Selection for UNbiased Ecophylogenomics (KITSUNE), a tool for assessing the empirically optimal k-mer length of any given set of genomes of interest for phylogenomic analysis via a three-step approach based on (1) cumulative relative entropy (CRE), (2) average number of common features (ACF), and (3) observed common features (OCF). Using KITSUNE, we demonstrated the feasibility and reliability of these measurements to obtain empirically optimal k-mer lengths of 11, 17, and ∼34 from large genome datasets of viruses, bacteria, and fungi, respectively. Moreover, we demonstrated a feature of KITSUNE for accurate species identification for the two
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.