In DNA/RNA as well as images, the recognition of patterns can offer extremely valuable insights. But, especially in high-throughput scenarios, computational cost can be prohibitive for most research projects. SciEngines' reconfigurable high performance computers can provide the resources needed for this type of analysis.
The discovery of regulatory sequences in DNA - called motif-finding - is one of the most computationally challenging problems in the field of bioinformatics. In fact, there are problem instances of motif-finding which are unsolvable by current approaches. There are two reasons making this problem so difficult:
- First, the parameters of a given problem instance (like sequence length, motif length, grade of mutation) can make it impossible to trace the motif in the background noise of the DNA, even if you had all the time you wanted to compute.
- Second, it is computationally expensive. So, a precise algorithm can fail to discover the motif in a given sequence because its execution time exceeds rational means.
We address both problems with an approach to motif finding that makes use of our massively parallel RIVYERA FPGA cluster to speed up the execution time. Less than 20 minutes are needed for a search of all motive instances in a Bacillus Subtilis genome file (5.9 Mbp). Please
if you are interested in motif search approaches allowing a new level of science.