41 lines
1.9 KiB
Markdown
41 lines
1.9 KiB
Markdown
---
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title: "Alignment-free sequence analysis"
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chunk: 4/4
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source: "https://en.wikipedia.org/wiki/Alignment-free_sequence_analysis"
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category: "reference"
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tags: "science, encyclopedia"
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date_saved: "2026-05-05T14:00:53.083806+00:00"
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instance: "kb-cron"
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---
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==== Iterated maps ====
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The use of iterated maps for sequence analysis was first introduced by HJ Jefferey in 1990 when he proposed to apply the Chaos Game to map genomic sequences into a unit square. That report coined the procedure as Chaos Game Representation (CGR). However, only 3 years later this approach was first dismissed as a projection of a Markov transition table by N Goldman. This objection was overruled by the end of that decade when the opposite was found to be the case – that CGR bijectively maps Markov transition is into a fractal, order-free (degree-free) representation. The realization that iterated maps provide a bijective map between the symbolic space and numeric space led to the identification of a variety of alignment-free approaches to sequence comparison and characterization. These developments were reviewed in late 2013 by JS Almeida in. A number of web apps such as https://github.com/usm/usm.github.com/wiki, are available to demonstrate how to encode and compare arbitrary symbolic sequences in a manner that takes full advantage of modern MapReduce distribution developed for cloud computing.
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== Comparison of alignment based and alignment-free methods ==
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== Applications of alignment-free methods ==
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Molecular phylogenetics
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Metagenomics
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Next generation sequence data analysis
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Epigenomics
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Barcoding of species
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Population genetics
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Horizontal gene transfer
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Sero/genotyping of viruses
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Allergenicity prediction
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SNP discovery
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Recombination detection
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== See also ==
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Sequence analysis
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Multiple sequence alignment
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Phylogenomics
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Bioinformatics
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Metagenomics
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Next-generation sequencing
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Population genetics
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SNPs
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Recombination detection program
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Genome skimming
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== References == |