A new method to find a set of energetically optimal RNA secondary structures.
We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown. In order to demonstrate the confidence of the program a test on four RNA sequences is performed. The method has computer time requirement proportional to N2, where N is the length of the sequence and retrieves a set of optimal free energy structures.
Benedetti
G
G
Department of Chemistry, University of Rome, Italy.
De Santis
P
P
Morosetti
S
S
D001482:Base Composition; D001483:Base Sequence; D008433:Mathematics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA; D012984:Software; D013816:Thermodynamics
D012313:RNA