242 research outputs found
A method for building simple physical models: representing the structures of nucleic acid
No full textAn improved low-resoln. phys. model for representing the structures of nucleic acids in presented. The models are inexpensive and easy to construct and show flexibility in application
A graph-topological approach to recognition of pattern and similarity in RNA secondary structures
No full textSecondary and tertiary RNA structures play an important role in many biological
processes. Therefore the necessity arises to find similar higher-order structures
for different but functionally homologous RNA sequences. We propose here a
graph-topological approach to the problem, which shows two main features:
simplified graph representation which allows the recognition of similarity of RNA
secondary structures with the same branching look despite minor differences. This
allows comparison among foldings from different sequences, and "pruning" of the
secondary structures not shared by all the sequences since the early stages of
the search. (b) The graph representation is encoded by the Randić topological
index, and the search for the folding similarity is reduced to checking the
identity of single numbers. These characteristics make this approach
significantly different, less depending on empirical criteria, and less
computationally heavy then previous methods, where the folding consensus has been
measured by an alignment procedure or correlation of strings representing the
secondary structures. Some U2 snRNA and viroid sequences are studied by this
approach, which is imbedded in our previous search method based on genetic
algorithms
A new method to find a set of energetically optimal RNA secondary structures.
No full textWe 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
Problemi di diagnosi prenatale ecografica di fronte a sospetta patologia malformativa polmonare. Relazione su due casi
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