---
title: "Alignment-free sequence analysis"
chunk: 4/4
source: "https://en.wikipedia.org/wiki/Alignment-free_sequence_analysis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T14:00:53.083806+00:00"
instance: "kb-cron"
---

==== Iterated maps ====
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.

== Comparison of alignment based and alignment-free methods ==

== Applications of alignment-free methods ==
Molecular phylogenetics
Metagenomics
Next generation sequence data analysis
Epigenomics
Barcoding of species
Population genetics
Horizontal gene transfer
Sero/genotyping of viruses
Allergenicity prediction
SNP discovery
Recombination detection

== See also ==
Sequence analysis
Multiple sequence alignment
Phylogenomics
Bioinformatics
Metagenomics
Next-generation sequencing
Population genetics
SNPs
Recombination detection program
Genome skimming

== References ==