Algorithmic Bioinformatics

Konrad Rudolph

Parallelism In The SeqAn Library

Academic Advisor: Knut Reinert , Manuel Holtgrewe
Degree: Master of Science (M.Sc.)
Degree: Mar 16, 2011
Status: finished


The purpose of this thesis is to allow "easy parallelism" in the SeqAn library. This will consist of identifying parts of the library where parallelization can be applied effectively and actually engineering (designing, implementing and evaluating) parts of the library to use parallelism. Common parallelization patterns should be extracted into a generalized framework/library that can then expose high-level parallelism to the users of SeqAn. The parallel execution of the string search algorithms in the module "find" as well as the algorithms for constructing indices are obvious candidate for parallelization. The parallel execution of string matching algorithms is a good starting point. Additionally, it allows the extension of the task to many interesting research questions, e.g. how to collect the results, how to process them etc.