A heuristic approach to RNA secondary structure prediction

The overall research context for this endeavor is the creation of an object-oriented representation scheme to facilitate phylogenetic analysis. As an initial and nontrivial subtask of this undertaking, we recognize the need to accomplish sequence alignment preceded by secondary structure prediction due to the length of the RNA strands with which we are working, namely 18S ribosomal RNA (rRNA). Secondary structure prediction is the focus of this paper. Though this topic has been addressed for the past two decades, our efforts concentrate on the introduction of heuristic techniques to make tractable an otherwise intractable problem. We introduce an object-oriented representation scheme to facilitate the utilization of biologist expertise and phylogenetic context into the arrival of secondary structures.