Name
Title | ||
|---|---|---|
A hardware accelerator for the alignment of multiple DNA sequences in forensic identification |
Abstract | ||
|---|---|---|
The comparison of DNA sequences is a classic problem in molecular biology. Forensic applications uses this comparison for personal identication. For instance, in the USA, the CODIS system has today 14.9 million DNA proles stored on its database. To accelerate the recurrent task to query into similar databases, this work presents a hardware acderator for the parallel alignment of multiple DNA sequences, aiming for the maximum throughput Each of these alignments is done using the Needleman-Wunsch algorithm which represents an optimal global technique for measuring the similarity between DNA sequences. The proposed accelerator architecture optimizes the use of hardware resources, the data access strategy and, as a result, memory bandwidth. The experiments were conducted using a synthetic DNA database with 8 million individuals, in which, each of them is represented using a set of 15 sequences with a length of 240 nucleotides. In this case study, a prototype of the proposed hardware accelerator using a single Stratix IV FPGA is running at the frequency of 280MHz and outperforms by tens of times consolidated software applications like SWIPE and FASTA which are running in a high performance GPP platform, as well as optimized GPU implementation in OpenCL. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1109/ASAP.2016.7760791 | 2016 IEEE 27th International Conference on Application-specific Systems, Architectures and Processors (ASAP) |
Keywords | Field | DocType |
hardware accelerator,DNA sequences,forensic identification,molecular biology,forensic applications,personal identication,CODIS system,DNA proles,Needleman-Wunsch algorithm,accelerator architecture,hardware resources,data access strategy,memory bandwidth,synthetic DNA database,Stratix IV FPGA,SWIPE,FASTA,frequency 280 MHz | Stratix,Memory bandwidth,Computer science,Parallel computing,Field-programmable gate array,SwIPe,Software,Hardware acceleration,Throughput,Data access | Conference |
ISSN | ISBN | Citations |
2160-0511 | 978-1-5090-1504-7 | 0 |
PageRank | References | Authors |
0.34 | 5 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Antonyus Pyetro do Amaral Ferreira | 1 | 8 | 3.21 |
| Joao G. M. Silva | 2 | 1 | 1.03 |
| Jefferson R. L. Anjos | 3 | 0 | 0.68 |
| Luiz H. A. Figueiroa | 4 | 0 | 0.68 |
| Edna Barros | 5 | 21 | 4.99 |
| Manoel Eusebio de Lima | 6 | 29 | 8.12 |
| Victor Wanderley Costa de Medeiros | 7 | 0 | 1.01 |