Parallel DNA Sequence Alignment Using FPGA Cross-Correlation
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Solution Overview
Problem
Conventional DNA sequencing algorithms are inefficient due to sequential operation, making it difficult to implement acceleration techniques and perform DNA sequencing analysis with increased efficiency.
Innovation Solution
The proposed solution involves parallelizing the computation by sliding DNA sequences against each other, using cross-correlation or convolution methods, and weighting matches to favor alignments closer to the center or ends of the sequences, allowing for parallel execution of multiple comparisons and recursive division of sequences to identify the longest continuous match.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional linear programming methods are used for DNA sequence alignment, then sequence matching accuracy is maintained, but processing time increases and efficiency decreases due to sequential operation requirements
Solution Approach 1:
The patent divides the DNA sequence alignment problem into independent segments that can be processed in parallel. By breaking down the sequential matrix computation into parallelizable units, the system maintains alignment accuracy while enabling concurrent processing across multiple computational cores, thereby improving productivity without sacrificing matching precision
Solution Approach 2:
The patent transforms the traditional sequential one-dimensional processing approach into a multi-dimensional parallel processing architecture. By implementing cross-correlation or convolution methods with multiple processing dimensions, the system can simultaneously evaluate multiple sequence alignments, reducing processing time while maintaining the accuracy of optimal path identification
2Productivity
If sequential computation methods are used, then algorithm simplicity is maintained, but acceleration techniques cannot be implemented effectively
Solution Approach 1:
The patent replaces the mechanical sequential execution model with a parallel computational system that uses cross-correlation or convolution operations. This substitution enables acceleration techniques by leveraging parallel processing capabilities of modern hardware, achieving computational speedup while managing complexity through standardized parallel operation patterns
3Measurement precision
If all matrix cells are computed sequentially, then complete path tracing accuracy is achieved, but processing efficiency is reduced
Solution Approach 1:
The patent performs preliminary computations in parallel to identify candidate optimal paths before final path tracing. By pre-computing potential alignment paths using parallel cross-correlation methods and then validating them, the system achieves both high throughput and accurate path identification, maintaining measurement precision while improving computation throughput
Data Source
AI summary
A field programmable gate array (FPGA) may: identify a continuous match of atoms between the search sequence and the reference sequence; divide the search sequence into a left portion of the search sequence that includes atoms before the continuous match of atoms in the search sequence, a center portion of the search sequence that includes the continuous match of atoms in the search sequence, and a right portion of the search sequence that includes atoms after the continuous match of atoms in the search sequence; match the left portion of the search sequence with the reference sequence; and match the right portion of the search sequence with the reference sequence.