Abstract: | Biomolecules exhibit a close interplay between structure and function. Therefore the growing number of RNA molecules with complex functions, beyond that of encoding proteins, has brought increased demand for RNA structure prediction methods. While prediction of tertiary structure is usually infeasible, the area of RNA secondary structures is an example where computational methods have been highly successful.
The first practical dynamic programming algorithms to predict the optimal secondary structure of an RNA sequence date back over 20 years (Zuker and Stiegler, 1981). Since then they have been extended to allow prediction of suboptimal structures (Zuker, 1989; Wuchty et al., 1999) and thermodynamic ensembles (McCaskill, 1990), which allow to assign a confidence level or ‘well definedness’ to the predictions (Zuker and Jacobson, 1995).
Recently, several methods have addressed the problem of predicting a consensus structure for a group of related RNA sequences (Gorodkin et al, 1997; Hofacker et al., 1998; Luck et al., 1999; Juan and Wilson, 1999; Knudsen, and Hein, 1999; Hofacker et. al., 2002). Such conserved structures are of particular interest, since conservation of structure in spite of sequence variation implies that the structure must be functionally important. By enhancing energy rules with sequence covariation these methods also obtain much better prediction accuracies.
Using genetic and molecular phylogeny techniques like PCR, up to sequencing the cytochrome’s b synthesizing gene, for different individuals of Cyprinus carpio L, 1758, sampled from two different populations, we were able to point out the existent differences between those analyzed individuals. All noted differences by comparing individuals from each population, as well as individuals having the origin in different populations, allowed the establishment of the general haplotype for the two studied populations as well as the characteristic haplotype for each population.
Towards pointing out the existing differences at the molecular level between individuals of the same species we followed the mRNA’s folding and it’s secondary space structure. |
