ReviewBriefings in bioinformatics2014
Sequence analysis by iterated maps, a review.
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 23 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
23 citing papers in PubMed, 47 citations in OpenAlex.
- Vertex Assignment for Frequency Chaos Game Representation of Proteins Affects Classification Performance.Computational and structural biotechnology journal · 2026Article
- Refining cancer prediction with DNA sequencing and combined machine learning approaches.Scientific reports · 2025Article
- Alignment-free viral sequence classification at scale.BMC genomics · 2025Article
- Changes in oscillatory patterns of microstate sequence in patients with first-episode psychosis.Scientific data · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- An efficient numerical representation of genome sequence: natural vector with covariance component.PeerJ · 2022Article
- Chaos game representation and its applications in bioinformatics.Computational and structural biotechnology journal · 2021Review
- RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation.Data in brief · 2020Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- Positional Correlation Natural Vector: A Novel Method for Genome Comparison.International journal of molecular sciences · 2020Article
- A novel numerical representation for proteins: Three-dimensional Chaos Game Representation and its Extended Natural Vector.Computational and structural biotechnology journal · 2020Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Application of Chaotic Laws to Improve Haplotype Assembly Using Chaos Game Representation.Scientific reports · 2019Article
- ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels.BMC genomics · 2019Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Review
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
- RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.BMC bioinformatics · 2017Article
- Additive methods for genomic signatures.BMC bioinformatics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.
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.