ABSTRACT
This chapter emphasizes the close relationship between structure and function in biology. The shape of macromolecules and of complexes of macromolecules determine the interactions that are allowed and, hence, the processes of life. The structural components of secondary structure are basepairs, bulges, interior loops, end loops, and multibranch loops. A hairpin is a structure with basepairs, bulges, interior loops, and exactly one end loop. The dynamic programming calculations are stored in a matrix and, in fact, are sometimes referred to as "matrix methods." Organizing these calculations in a way which allows visualization of the associated RN A structures is a useful device. The sequences are placed into an initial alignment. Instead of one window as in multiple sequence consensus word analysis, we put two nonoverlapping windows onto the sequences. Once a helix is found and the ambiguities are resolved, it can be locked into place and the search continued. Ambiguities include alternate choices of helicies in a sequence.
