ReviewBriefings in bioinformatics2014
Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.
Review in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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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.
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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
58 citing papers in PubMed.
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- The grand biological universe: A comprehensive geometric construction of genome space.Innovation (Cambridge (Mass.)) · 2025Article
- Article
- Reconstruction of masked sequencesPeerJ · 2025Article
- The optimal metric for viral genome space.Computational and structural biotechnology journal · 2024Article
- Article
- Application of Feature Definition and Quantification in Biological Sequence Analysis.Current genomics · 2023Article
- Learning to Learn: How to Continuously Teach Humans and Machines.... IEEE International Conference on Computer Vision workshops. IEEE International Conference on Computer Vision · 2023Article
- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
- Alignment-free comparison of metagenomics sequences via approximate string matching.Bioinformatics advances · 2022Article
- Use of an Alignment-Free Method for the Geographical Discrimination of GTPVs Based on the GPCR Sequences.Microorganisms · 2021Article
- Article
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.PloS one · 2021Article
- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level.BMC bioinformatics · 2020Article
- Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.Systematic biology · 2020Article
- Whole-GenomeGenes · 2020Article
- KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.Frontiers in bioengineering and biotechnology · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression.
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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.