The main areas of our research are: DNA sequencing and assembling (including design of algorithms for the NGS sequencers); protein & RNA structure analysis and modeling (including automatic tertiary structure prediction tools); nanotechnology and DNA computing.
GRASShopPER (GPU overlap GRaph ASSembler using Paired End Reads) is the novel assembly method that follows the approach of overlap–layout–consensus (OLC). In the method, a very efficient GPU implementation of the exact reads alignment algorithm has been used for calculating the scores and shifts on the arcs of the graph. Two-part fork detection strategy has been introduced, which highly reduces misassembly rate in the resulting contigs. The first part is carried out during the graph traversal. In the second part, a greedy hyper-heuristic identifies undetected forks on the basis of paired-end reads information. The results of computational experiments show high coverage of the tested genome.