Sequences are omnipresent. Texts and programs, genes and proteins, speech and image signals are represented as character strings over a finite alphabet. The algorithmic questions are correspondingly diverse. Often, the amount of data is very large, so that the complexity of the algorithms used to solve the problem is of crucial practical importance. The lecture covers efficient algorithms for searching, analyzing, and comparing sequences. Many of these algorithms are motivated by biological questions. However, they also find applications in other areas, such as searching large collections of XML documents.

The lecture contains numerous cross-references to data compression. For example, novel index data structures are based on the Burrows-Wheeler transformation, which also plays a crucial role in newer data compression methods.

 

Literature
E. Ohlebusch: Bioinformatics Algorithms, Oldenbusch Verlag, 2013.
D. Gusfield: Algorithms on Strings, Trees, and Sequences, Cambridge University Press, 1997.