ArticleBMC bioinformatics2009
Biological sequences as pictures: a generic two dimensional solution for iterated maps.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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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Who cites it
10 citing papers in PubMed.
- Modeling Human Frailty with a Smart Home-Based Approximation of Entropy.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- Chaos game representation and its applications in bioinformatics.Computational and structural biotechnology journal · 2021Review
- Additive methods for genomic signatures.BMC bioinformatics · 2016Article
- An investigation into inter- and intragenomic variations of graphic genomic signatures.BMC bioinformatics · 2015Article
- Sequence analysis by iterated maps, a review.Briefings in bioinformatics · 2014Review
- Information theory applications for biological sequence analysis.Briefings in bioinformatics · 2014Review
- Fractal MapReduce decomposition of sequence alignment.Algorithms for molecular biology : AMB · 2012Article
- Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.Algorithms for molecular biology : AMB · 2012Article
- New method for comparing DNA primary sequences based on a discrimination measure.Journal of theoretical biology · 2010Article
- A web server for interactive and zoomable Chaos Game Representation images.Source code for biology and medicine · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundRepresenting symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR). The usefulness of this representation goes beyond the convenience of a scale independent representation. It provides a variable memory length representation of transition. This includes the representation of succession with non-integer order, which comes with the promise of generalizing Markovian formalisms. The original proposal targeted genomic sequences only but since then several generalizations have been proposed, many specifically designed to handle protein data.
resultsThe challenge of a general solution is that of deriving a bijective transformation of symbolic sequences into bi-dimensional planes. More specifically, it requires the regular fractal nesting of polygons. A first attempt at a general solution was proposed by Fiser 1994 by using non-overlapping circles that contain the polygons. This was used as a starting point to identify a more efficient solution where the encapsulating circles can overlap without the same happening for the sequence maps which are circumscribed to fractal polygon domains.
conclusionWe identified the optimal inscribed packing solution for iterated maps of any Biological sequence, indeed of any symbolic sequence. The new solution maintains the prized bijective mapping property and includes the Sierpinski triangle and the CGR square as particular solutions of the more encompassing formulation.
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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.