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