title: 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.
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.
authors.affiliation: Istituto Nazionale di Alta Matematica, Piazzale A. Moro 5 I-00185 Roma, Italy. menconi@mail.dm.unipi.it
authors.forename: Giulia
authors.initials: G
authors.lastname: Menconi
authors.forename: Aldamaria
authors.initials: A
authors.lastname: Puliti
authors.forename: Isabella
authors.initials: I
authors.lastname: Sbrana
authors.forename: Valerio
authors.initials: V
authors.lastname: Conti
authors.forename: Roberto
authors.initials: R
authors.lastname: Marangoni
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence / Q000502:physiology*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000145:classification*; D044962:Data Compression; D057225:Data Mining / Q000379:methods; D016678:Genome / Q000235:genetics*; D006801:Humans; D051379:Mice; D009690:Nucleic Acid Conformation; D064529:Receptor, Metabotropic Glutamate 5; D018094:Receptors, Metabotropic Glutamate / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D064529:Receptor, Metabotropic Glutamate 5; D018094:Receptors, Metabotropic Glutamate; C104077:metabotropic glutamate receptor type 1; D004247:DNA