Home

The goal of this thesis is to develop a sequence alignment algorithm for circular sequences based on the FM-Index data structure. This work will involve working with algorithms and data structures for indexing and string matching and consists on the implementation and testing of a tool to perform string alignment between large numbers of circular sequences; The working alphabet is the regular DNA letters (A, C, G, T, and N) and implementation should be done in a fast low-level programming language such as C or C++. Additional multi-threading and parallelization is optional but welcome. A visualization component for the final alignment is not required, but also welcome.