Vector-based method for visualizing secondary structure of RNA molecules

A method for visualizing a secondary structure of a single-stranded RNA molecule, which uses a vector and vector space to determine the direction and space of structural elements and which includes the steps of:

• regularizing said secondary structure, wherein the regularizing said secondary structure step is carried out by transforming the secondary structure into a regular secondary structure through the introduction of at least one artificial base so that the structure does not contain any bulge loop, dangling end, or helices directly adjacent to each other, and then storing the regularized secondary structure in a data structure which plays the role of an organization object;
• building data structures, wherein the building data structure step is implemented by identifying structural elements from the organization object and constructing data structures of a secondary structure object and a draw list object for each of the identified structural elements;
• determining positioning priority, wherein said determining positioning priority step is comprised of computing the sizes of all loops in the constructed data structure, determining the positioning priorities of all structural elements including helices, and storing the determined priorities in a data structure, which is a priority queue;
• and
• positioning and drawing structural elements, wherein the positioning and drawing structural elements step is carried out by computing open and allowed vector spaces and a feasible vector with the starting point being a structural element with the highest drawing priority, positioning a structural element in the direction of the feasible vector, computing the coordinates of structural element-constituting bases for each of the positioned structural elements, and displaying them.