title: RNA partial degradation problem: motivation, complexity, algorithm.
abstract: Studies conducted during the last decade unexpectedly revealed several new biological functions of RNA molecules. The involvement of RNA in many complex processes requires highly effective systems controlling its accumulation. In this context, the mechanisms of degradation appear as one of the most important factors influencing RNA activity. Here, we present our first attempt to describe the RNA degradation process using bioinformatics methods. Based on the obtained data, we propose a formulation of a new problem, called RNA Partial Degradation Problem (RNA PDP) and the algorithm that is capable of reconstructing an RNA molecule using the results of biochemical analysis of its degradation. In addition, we present the results of biochemical experiments and computational tests.
authors.affiliation: Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Blazewicz
authors.forename: Marek
authors.initials: M
authors.lastname: Figlerowicz
authors.forename: Marta
authors.initials: M
authors.lastname: Kasprzak
authors.forename: Martyna
authors.initials: M
authors.lastname: Nowacka
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Rybarczyk
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism*; D020871:RNA Stability
chemical_list: D012313:RNA