Dynamic programming (DP) algorithms have become indispensable in computational biology, addressing problems that range from sequence alignment and phylogenetic inference to RNA secondary structure ...

Genome assembly algorithms are sets of well defined procedures for reconstructing DNA sequences from large numbers of shorter DNA sequence fragments. Fragments are aligned against one another and ...

We will pursue the dynamic programming approach and give computational experi- ence for several extensions of the basic model. We begin with some simple, but prac- tically important, extensions ...