Article

Article title IMPLEMENTATION OF THE DNA ASSEMBLY PROBLEM ON RECONFIGURABLE COMPUTER SYSTEMS
Authors А. I. Levina, E. E. Semernikova, D. A. Sorokin
Section SECTION IV. RECONFIGURABLE AND NEURAL NETWORK COMPUTING SYSTEMS
Month, Year 08, 2018 @en
Index UDC 004.273
DOI 10.23683/2311-3103-2018-8-204-212
Abstract The paper deals with research of methods and tools for the problem of DNA assembly, which provide considerable reducing of the processing time for the specified accuracy in comparison with other methods and tools. We are considering using of reconfigurable computer systems for the assembly problems. As an example we use implementation of a key procedure of the algorithm of genome assembly Velvet Assembler – a procedure of contigs generation VelvetH. The base of the Velvet Assembler is a new generation method which implies generation of a de Bruijn graph, and, as a result, causes considerably variable density of data flows in the nondeterministic polynomial time complete problem of DNA assembly. That is why, in addition to the technology of structural-procedural organization of calculations, which is traditional for reconfigurable computer systems, we used special methods of synthesis of parallel-pipeline applications to provide a possibility in principle of implementation of such problems on reconfigurable computer systems. For evaluation of efficiency of reconfigurable computer systems use, we have developed, using a procedure VelvetН, a parallel-pipeline application which assembles a genome from short reads of a DNA Staphylococcus aureus. We have taken data from the database Sequence Read Archive from the website National Center for Biotechnology Information. The parallel-pipeline application was tested on a reconfigurable computer system “Tertius”, designed on the base of four Xilinx Kintex UltraScale XCKU 095 FPGAs. Use of this reconfigurable computer system provides 24-fold (and more) reduction of the execution time of the contig generation procedure for the DNA assembly problem against the existing analogs. Due to this we can conclude, that use of reconfigurable computer systems for implementation of the DNA assembly problem is a promising direction, which requires further scientific and technical research.

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Keywords Field-programmable gate array; reconfigurable computing structure; de novo sequencing assembly; computing acceleration.
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