Name
Abstract | ||
|---|---|---|
Recent advances in molecular sequencing technology have given rise to novel algorithms for simultaneously aligning short sequence reads to reference sequence alignments and corresponding evolutionary reference trees. We present a complete hardware/software implementation for the acceleration of a program called PaPaRa, a newly introduced dynamic programming algorithm for this purpose. We verify the correctness of the proposed architecture on a real FPGA and introduce a straight-forward communication protocol(using gigabit ethernet) for seamless integration with the encapsulating steering software that is executed on a PC processor. The hardware description and the software implementation are freely available for download. When mapped to a Virtex 6 FPGA, our reconfigurable architecture can compute 133.4 billion cell updates per second for the novel, tree-based alignment kernel of PaPaRa. Compared to PaPaRa, running on a 3.2GHz Intel Core i5 CPU, we obtain speedups for the alignment kernel, that range between 170 and 471. For the entire application, that is, the alignment kernel and the trace-back step, we obtain speedups between 74 and 118. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1109/FCCM.2011.13 | FCCM |
Keywords | Field | DocType |
accelerating phylogeny-aware short dna,reference sequence alignment,corresponding evolutionary reference tree,complete hardware,software implementation,hardware description,read alignment,novel algorithm,tree-based alignment kernel,encapsulating steering software,alignment kernel,proposed architecture,communication protocol,multiple alignment,dna,computer architecture,acceleration,field programmable gate array,dynamic programming algorithm,field programmable gate arrays,phylogeny,fpga,sequence alignment,dynamic programming,genetic engineering,kernel | Dynamic programming,Computer science,Correctness,Parallel computing,Field-programmable gate array,Real-time computing,Software,Gigabit Ethernet,Virtex,Multiple sequence alignment,Communications protocol | Conference |
Citations | PageRank | References |
5 | 0.54 | 15 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Nikolaos Alachiotis | 1 | 120 | 17.72 |
| Simon A. Berger | 2 | 71 | 7.46 |
| Alexandros Stamatakis | 3 | 995 | 96.27 |