ArticleAnnual review of biomedical data science2018
Alignment-Free Sequence Analysis and Applications.
Article in Annual review of biomedical data science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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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.
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Who cites it
51 citing papers in PubMed.
- Alignment-freeJournal of clinical microbiology · 2026Article
- A reproducible compartment-aware k-mer set-algebra and MAW workflow for plant genomes maps contrasting nuclear-organelle sharing landscapes in Arabidopsis and rice.Plant methods · 2026Article
- A novel dynamic part-wise direct and complementary template matching approach for DNA sequence similarity identification.Molecular genetics and genomics : MGG · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- Reducing haystacks to needles-ViralClust: a Nextflow pipeline to cluster viral sequences.GigaScience · 2026Article
- Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans.Virus evolution · 2026Article
- Genomic evolution of SARS-CoV-2 delta variants pre- and post-omicron emergence using alignment-free machine learning models.PloS one · 2026Article
- Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling.Systematic biology · 2025Article
- Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR genomics and bioinformatics · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.Environmental microbiome · 2025Article
- Evaluation of antioxidant activity of brown macroalgae found in Lampung Bay, Indonesia and molecular identification using DNA barcode cox1 BLAST.Molecular biology reports · 2025Article
- Review
- An alignment- and reference-free strategy usingMycology · 2025Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data.PLoS computational biology · 2024Review
- Detecting genetic gain and loss events in terms of protein domain: Method and implementation.Heliyon · 2024Article
- Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques.BMC bioinformatics · 2024Article
- New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.BMC bioinformatics · 2023Article
- (Bioinformatics advances · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Genome and metagenome comparisons based on large amounts of next generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they contribute significantly to genome and metagenome comparison. Recently, novel statistical approaches have been developed for the comparison of both long and shotgun sequences. These approaches have been applied to many problems including the comparison of gene regulatory regions, genome sequences, metagenomes, binning contigs in metagenomic data, identification of virus-host interactions, and detection of horizontal gene transfers. We provide an updated review of these applications and other related developments of word-count based approaches for alignment-free sequence analysis.
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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.