Mr. Wust will be at Fraunhofer FIRST from February 17 till March 19 for a scientific mission in the realm of Project SNOW. During this scientific mission, Mr. Wust will investigate strategies to parallelize the procedure of DNA sequencing --- currently one of the most significant application areas for the project.
The most common method for sequencing nucleotides of large pieces of DNA is the Shotgun Sequencing. This method splits DNA into several random pieces. The sequence of bases in these pieces is then read by an automated sequencing machine. After this step is performed, it is necessary to reassemble such fragments in their original order. This activity clearly calls for high-performance computing.
Some algorithms have been developed to perform the task of DNA fragment reassembly. These algorithms take the unordered sequences of bases as input and try to reorder them in order to reproduce the original sequence. One major problem of this process is that the input dataset may present errors. Theses errors consist of badly added, deleted or miscalled nucleotides. Although the problem of DNA reassembly falls in the class of the NP-hard problems, empirically it can be efficiently solved by sufficiently powerful computations.
The Fraunhofer FIRST Institute, a German partner of SNOW, has a large experience on parallelization of complex algorithms. It would be very profitable to take advantage of this know-how for the definition of a parallelization strategy for the DNA reassembly algorithm. Additionally, this mission will bring LISHA's expertise on the theme to the German partners.