A necklace algorithm to determine the growth function of trinucleotide circular codes

Matthieu Luc Herrmann, Christian Michel, Benoît Sugmeyer

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Circular codes are mathematical objects studied in combinatorics - theoretical computer science, and theoretical biology. So far, there is no close formulas allowing to determine the growth function (number and list) of circular codes. This combinatorial problem can only be solved by an algorithmic approach. We propose a new algorithm based on a necklace proposition to determine the growth function of trinucleotide circular codes, a trinucleotide being a word of 3 letters on a 4-letter alphabet. This necklace algorithm, unique in its class, can be extended in future to the analysis of codes, e.g. circular codes, containing words greater than 3 letters and also over larger alphabets.
Original languageEnglish
Pages (from-to)1-40
JournalJournal of Applied Mathematics & Bioinformatics
Publication statusPublished - 2013
Externally publishedYes

Keywords

  • Circular code
  • Genetic code
  • necklace algorithm
  • combinatorial algorithm

Cite this

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abstract = "Circular codes are mathematical objects studied in combinatorics - theoretical computer science, and theoretical biology. So far, there is no close formulas allowing to determine the growth function (number and list) of circular codes. This combinatorial problem can only be solved by an algorithmic approach. We propose a new algorithm based on a necklace proposition to determine the growth function of trinucleotide circular codes, a trinucleotide being a word of 3 letters on a 4-letter alphabet. This necklace algorithm, unique in its class, can be extended in future to the analysis of codes, e.g. circular codes, containing words greater than 3 letters and also over larger alphabets.",
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A necklace algorithm to determine the growth function of trinucleotide circular codes. / Herrmann, Matthieu Luc; Michel, Christian; Sugmeyer, Benoît.

In: Journal of Applied Mathematics & Bioinformatics, 2013, p. 1-40.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - A necklace algorithm to determine the growth function of trinucleotide circular codes

AU - Herrmann, Matthieu Luc

AU - Michel, Christian

AU - Sugmeyer, Benoît

PY - 2013

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N2 - Circular codes are mathematical objects studied in combinatorics - theoretical computer science, and theoretical biology. So far, there is no close formulas allowing to determine the growth function (number and list) of circular codes. This combinatorial problem can only be solved by an algorithmic approach. We propose a new algorithm based on a necklace proposition to determine the growth function of trinucleotide circular codes, a trinucleotide being a word of 3 letters on a 4-letter alphabet. This necklace algorithm, unique in its class, can be extended in future to the analysis of codes, e.g. circular codes, containing words greater than 3 letters and also over larger alphabets.

AB - Circular codes are mathematical objects studied in combinatorics - theoretical computer science, and theoretical biology. So far, there is no close formulas allowing to determine the growth function (number and list) of circular codes. This combinatorial problem can only be solved by an algorithmic approach. We propose a new algorithm based on a necklace proposition to determine the growth function of trinucleotide circular codes, a trinucleotide being a word of 3 letters on a 4-letter alphabet. This necklace algorithm, unique in its class, can be extended in future to the analysis of codes, e.g. circular codes, containing words greater than 3 letters and also over larger alphabets.

KW - Circular code

KW - Genetic code

KW - necklace algorithm

KW - combinatorial algorithm

M3 - Article

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JO - Journal of Applied Mathematics & Bioinformatics

JF - Journal of Applied Mathematics & Bioinformatics

SN - 1792-6939

ER -