Mutation model for nucleotide sequences based on crystal basis.
A nucleotide sequence is identified, using a two (four)-letter alphabet, by the the labels of a vector state of an irreducible representation of Uq-->0(sl(2)) (Uq-->0(sl(2) plus sign in circle sl(2))). A master equation for the distribution function is written, where the intensity of the one-spin flip is assumed to depend on the variation of the labels of the state. In the two-letter approximation, the numerically computed equilibrium distribution for short sequences is fitted nicely by a Yule distribution, which is the observed distribution of the ranked short oligonucleotides frequency in DNA. The four-letter alphabet description, applied to the codons, is able to reproduce the form of the fitted rank-ordered usage frequencies distribution.
Minichini
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Dipartimento di Scienze Fisiche, Università di Napoli "Federico II", I-80126 Naples, Italy. minichini@na.infn.it
Sciarrino
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D001483:Base Sequence; D003062:Codon / Q000235:genetics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D008956:Models, Chemical; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
D003062:Codon; D009711:Nucleotides; D004247:DNA