Genome characterization through dichotomic classes: an analysis of the whole 22 chromosome 1 of a. thaliana (Articolo in rivista)

Type
Label
  • Genome characterization through dichotomic classes: an analysis of the whole 22 chromosome 1 of a. thaliana (Articolo in rivista) (literal)
Anno
  • 2013-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.3934/mbe.2013.10.199 (literal)
Alternative label
  • Properzi E., Giannerini S., Gonzalez, Diego L., Rosa R. (2013)
    Genome characterization through dichotomic classes: an analysis of the whole 22 chromosome 1 of a. thaliana
    in Mathematical biosciences and engineering
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Properzi E., Giannerini S., Gonzalez, Diego L., Rosa R. (literal)
Pagina inizio
  • 199 (literal)
Pagina fine
  • 219 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 10 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali
  • 21 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 1 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Dipartimento di Statistica, UNIBO, CNR-IMM (literal)
Titolo
  • Genome characterization through dichotomic classes: an analysis of the whole 22 chromosome 1 of a. thaliana (literal)
Abstract
  • In this article we show how dichotomic classes, binary variables naturally derived from a new mathematical model of the genetic code, can be used in order to characterize different parts of the genome. In particular, we analyze and compare different parts of whole chromosome 1 of Arabidopsis thaliana: genes, exons, introns, coding sequences (CDS), intergenes, untrans- lated regions (UTR) and regulatory sequences. In order to accomplish the task we encode each sequence in the 3 possible reading frames according to the denitions of the dichotomic classes (parity, Rumer and hidden). Then, we perform a statistical analysis on the binary sequences. Interestingly, the results show that coding and non-coding sequences have different patterns and proportions of dichotomic classes. This suggests that the frame is important only for coding sequences and that dichotomic classes can be useful to recog- nize them. Moreover, such patterns seem to be more enhanced in CDS than in exons. Also, we derive an independence test in order to assess whether the per- centages observed could be considered as an expression of independent random processes. The results conrm that only genes, exons and CDS seem to possess a dependence structure that distinguishes them from i.i.d sequences. Such in- formational content is independent from the global proportion of nucleotides of a sequence. The present work conrms that the recent mathematical model of the genetic code is a new paradigm for understanding the management and the organization of genetic information and is an innovative tool for investigating informational aspects of error detection/correction mechanisms acting at the level of DNA replication. (literal)
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