Dynamic programming is an efficient technique to solve combinatorial search and
optimization problem. There have been many parallel dynamic programming algorithms …

Background RNA secondary structure prediction is a compute intensive task that lies at the
core of several search algorithms in bioinformatics. Fortunately, the RNA folding …

Polyhedral compilation techniques have proven to be a powerful tool for optimization of
dense array codes. In particular, their ability to tile imperfectly nested loops has provided …

Dynamic programming (DP) is a popular technique which is used to solve combinatorial
search and optimization problems. This paper focuses on one type of DP, which is called …

Dynamic programming has been one of the most efficient approaches to sequence analysis
and structure prediction in biology. However, their performance is limited due to the drastic …

Dynamic programming (DP) is a popular and efficient technique in many scientific
applications such as computational biology. Nevertheless, its performance is limited due to …

Background An RNA primary structure, or sequence, is a single strand considered as a
chain of nucleotides from the alphabet AUGC (adenine, uracil, guanine, cytosine). The …

Dynamic programming (DP) is an effective technique for many search and optimization
problems. However, the high arithmetic complexity limits its extensive use. Although modern …

Dynamic programming approach solves complex problems efficiently by breaking them
down into simpler sub-problems, and is widely utilized in scientific computing. With the …

Publisher Summary This chapter presents an implementation of the main kernel in the
widely used RNA folding package Unafold. Its key computation is a dynamic programming …