Parallel architecture for DNA sequence inexact matching with Burrows-Wheeler Transform

Xin, Y., Liu, B., Min, B., Li, W. X., Cheung, R. C., Fong, A. S., & Chan, T. F. (2013). Parallel architecture for DNA sequence inexact matching with Burrows-Wheeler Transform. Microelectronics Journal, 44(8), 670-682.


The Burrows-Wheeler Transform (BWT) based methodology seems ideally suited for DNA sequence alignment due to its high speed and low space complexity. Despite being efficient in exact matching, the application of BWT in inexact matching still has problems due to the excessive backtracking process. This paper presents a hardware architecture for the BWT-based inexact sequence mapping algorithm using the Field Programmable Gate Array (FPGA). The proposed design can handle up to two errors, including mismatches and gaps. The original recursive algorithm implementation is dealt with using hierarchical tables, and is then parallelized to a large extension through a dual-base extension method. Extensive performance evaluations for the proposed architecture have been conducted using both Virtex 6 and Virtex 7 FPGAs. This design is considerably faster than a direct implementation. When compared with the popular software evaluation tool BWA, our architecture can achieve the same match quality tolerating up to two errors. In an execution speed comparison with the BWA aln process, our design outperforms a range of CPU platforms with multiple threads under the same configuration conditions.