RNA Sequence Structure Alignment

A, C, G, and U. It is a generally single-stranded molecule where the
bases form hydrogen bonds within the same molecule leading to
structure formation. In comparing different homologous RNA
molecules it is important to consider both the base sequence and
the structure of the molecules.
Traditional alignment algorithms can only account for the
sequence of bases, but not for the base pairings.
Considering the structure leads to significant computational
problems because of the dependencies introduced by the base pairings.
In this paper we address the problem of optimally
aligning a given RNA sequence of unknown structure to one of
known sequence and structure.
We phrase the problem as an integer linear program and
then solve it using methods from polyhedral combinatorics.
In our computational experiments we could solve large problem
instances -- 23S ribosomal RNA with more than 1400 bases -- a size
intractable for former algorithms.