A top-down linguistic approach to the analysis of genomic sequences: The metabotropic glutamate receptors 1 and 5 in human and in mouse as a case study

Giulia Menconi, Aldamaria Puliti, Isabella Sbrana, Valerio Conti, Roberto Marangoni

Research output: Contribution to journalArticle

Abstract

This paper presents a top-down strategy to detect features in genomic sequences. The strategy's core is to exploit dictionary-based compression algorithms and analyse the content of the automatically generated dictionary. We classify the different over-represented segments and in the case study we correlate them to experimentally identified or theoretically forecasted biological features. A large spectrum analysis reveals that the only feature co-located with the a priori extracted segments is the torsional flexibility of DNA, while non-B DNA configurations are anti-localized and other features are mostly independent of the extracted sequences. This analysis unravels complex relationships between the linguistic structures investigated under our approach and some known biological features.

Original languageEnglish
Pages (from-to)134-142
Number of pages9
JournalJournal of Theoretical Biology
Volume270
Issue number1
DOIs
Publication statusPublished - Feb 7 2011

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Keywords

  • Combinatorics on words
  • DNA flexibility
  • Over-represented segments

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Modelling and Simulation
  • Statistics and Probability
  • Applied Mathematics

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