1. DNA N-gram analysis framework (DNAnamer): A generalized N-gram frequency analysis framework for the supervised classification of DNA sequences.
- Author
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Malamon JS
- Abstract
In 1948, Claude Shannon published a mathematical system describing the probabilistic relationships between the letters of a natural language and their subsequent order or syntax structure. By counting unique, reoccurring sequences of letters called N-grams, this language model was used to generate recognizable English sentences from N-gram frequency probability tables. More recently, N-gram analysis methodologies have been successfully applied to address many complex problems in a variety of domains, from language processing to genomics. One such example is the common use of N-gram frequency patterns and supervised classification models to determine authorship and plagiarism. In this paradigm, DNA is a language model where nucleotides are analogous to the letters of a word and nucleotide N-grams are analogous to the words of a sentence. Because DNA contains highly conserved and identifiable nucleotide sequence frequency patterns, this approach can be applied to a variety of classification and data reduction problems, such as identifying species based on unknown DNA segments. Other useful applications of this methodology include the identification of functional gene elements, microorganisms, sequence contamination, and sequencing artifacts. To this end, I present DNAnamer, a generalized and extensible methodological framework and analysis toolkit for the supervised classification of DNA sequences based on their N-gram frequency patterns., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: John Stephen Malamon reports administrative support was provided by 10.13039/100014450University of Colorado Anschutz Medical Campus School of Medicine. John Stephen Malamon reports a relationship with University of Colorado Anschutz Medical Campus School of Medicine that includes: employment. John Stephen Malamon has patent pending to N/A. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Author. Published by Elsevier Ltd.)
- Published
- 2024
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