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 (1) , Aldamaria Puliti (2, 3) , Isabella Sbrana (4) , Valerio Conti (2) , Roberto Marangoni (5, 6)

1 Istituto Nazionale di Alta Matematica
2 Gaslini Institute
3 Dipartimento di Scienze Pediatriche
4 Dipartimento di Biologia
5 Dipartimento di Informatica
6 Istituto di Biofisica

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 analyze 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 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.

Mots clés: 68R15; 62P10; 92B05

Giulia Menconi, Aldamaria Puliti, Isabella Sbrana, Valerio Conti, Roberto Marangoni. 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. Journal of Theoretical Biology, 2011, 270 (1), pp.134. ⟨10.1016/j.jtbi.2010.11.020⟩. ⟨hal-00656342⟩